Activities

Autumn 2022

Frontiers in post-genome studies, 5 ECTS

Sep 26^th to Oct 14^th

We are happy to announce this exciting course that will introduce you to prominent researchers and give you practical skills for competitive grant writing.

During the course part, you will meet world leading experts from various fields working with diverse model systems/organisms. The course will highlight novel methods and technologies and serve as inspiration for the career development and grant writing workshops.

The workshops will cover critical aspects of competitive grant writing, including CV development, evaluation metrics, budgeting, working in prisma and opportunities/career paths. Participants will undertake exercises and write an abbreviated grant proposal to hone their science communication skills.

The course will run in-person at the SLU Biocenter, Uppsala. Final lecture dates may change due to guest speaker travel and availability.

The course is organized by Adrian Dauphinee on behalf of the SLU research school “Focus on Food and Biomaterials” in collaboration with the research school “Organism Biology”.

Please register by sending a note to Adrian Dauphinee adrian.dauphinee@slu.se with cc: to galia.zamaratskaia@slu.se .

Link to syllabus

Link to schedule

Link to Flyer

Visualize your Science, 4 ECTS (PNG0073)

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake. 
 
The course is software independent and will cover things like use of colors, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know 

- How to create beautiful and credible scientific posters.

- How to use professional illustration software to illustrate your research.

- Where to find images, if you cannot draw them yourself.

- How to create images that are simple but yet informative.

The course runs on part time from September 13th to November 18th. For more info about the course, see the syllabus and the schedule attached. You can also visit the course home page at https://www.visualizeyourscience.com/pages/vys-course.

The course represents a mix of online theory and drawing tutorials complemented with four feedback meetings. All joint sessions will be in form of on-line sessions but you can also attend two of the sessions face-to-face at campus.

The course is organized and taught by Andreas Dahlin and his team at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see the short résumé attached.

The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For binding registration on first serve basis (student number limited to 20), send an e-mail before September 6th to Katarina.Landberg@slu.se indicating your name, department and position. In principle, all costs for the course are covered by the research school Organism Biology. The one exception is if a registrant fail to attend the course without informing the organizer in due time. If this happens, the person must pay the actual course fee of 625€.   

Link to syllabus

Link to schedule

Link to résumé about organizer

Organism Biology PhD course:

Analysis of High Throughput Sequencing RNA-Seq Data (3^rd edition)

(November 7 ^th-8^th); November 14^th - November 18^th; (November 25^th)

High Throughput Sequencing (HTS) technologies and in particular Next Generation Sequencing (NGS) have revolutionized the way we conduct gene expression analysis. In comparison to micro-array-based methods, NGS has unleashed an almost unlimited power to perform gene expression analysis, for a similar price and with faster, more comprehensive, more efficient and more reproducible characteristics. Rapidly, the data generation rate has exceeded the analytical capabilities and data analysis has become the major bottleneck in gene expression studies.

The SLU Bioinformatics Infrastructure (SLUBI) is organizing an advanced course for the Organism Biology Research School, aimed at PhD students, that has the objective to help addressing this problem by (i) helping participants critically assess the challenges faced in the HTS field, (ii) developing efficient communication skill with bioinformatician, and (iii) training students in analyzing HTS data. For detailed info about the course, please see the syllabus and preliminary schedule attached.

The aims of this course are to:

• familiarize the participants with advanced RNA-Seq data analysis methodologies and how biological knowledge can be gained from these by illustrating different analyses approaches
• allow the participants to acquire computational competences about latest RNA-Seq analytical approaches and related statistical methods
• expose the participants to modern computing technologies, as the computer hands-on of the course will be performed using cloud computing resources
• develop the participants’ awareness to critically reflect onto RNA-Seq analysis strengths and weaknesses
• enable participants to perform the analysis of their own data (in stance of the exemplary dataset otherwise available)

The course has one main module, and two optional modules (two and one ECTs credits each, respectively). The main module covers the analysis of RNA-Seq data, while the first optional module is an introduction to the Unix and R environments to give attendees the necessary admission requirements for the main module. The second optional module is a follow-up for attendees to apply the knowledge gained from the main module content on their own data. The course will provide two to four ECTS credits depending on the selected modules, as follows:

Module 1 (optional) 2 days - 1 ECTS

Module 2 (mandatory) 5 days - 2 ECTS

Module 3 (optional) 1 day - 1 ECTS

The course will be conducted online only. However, if students wish so, they can organise themselves in groups and join using one of the teaching facilities available at SLU.

The course has a maximum number of participants is 20. PhD students will be prioritised, but admission will be on a first-come, first-served basis, provided that the minimal requirements are met. Application deadline: Nov 1^st. To register, follow this link: https://forms.gle/7TJDqLkYok7kmet17.

If you have any question, please contact the course leaders (nicolas.delhomme@slu.se, iryna.shutava@slu.se) or the slack channel #organism-biology-research-school-rna-seq-course of the slubi-workspace.slack.com workspace.

All the best,

Katarina Landberg, Organism Biology coordinator

Link to syllabus

Link to scheduele

To communicate science

POG0086 • 2,0 credits • Uppsala • 20 sep - 16 nov 2022

Would you like to learn how to communicate your science to a wider audience? During this online course the participants will learn about different channels for research communication of popular science and how they can be used. We will cover for example popular science writing, blogging, electronic and social media. The training will be accomplished by lectures, seminars and practical exercises where the students can train their new skills.

With a mix of lecturers from both the university environment, as well as journalists from "the field" we aim to create an open course climate where different views and experiences can meet. The foundation of the course is dialogue, activity and different practical exercises.

The course is organised jointly by the NJ Research Schools (Ecology - basics and applications, Focus on Food and Biomaterials, Focus on Soils and Water, Organism biology, Society and Landscape Research School, Sustainable Biomass System, Social Science Perspectives on Sustainable Development) and the divisions of Planning and Communication.

For application, please visit: https://internt.slu.se/en/support-services/education/doctoral-education1/doctoral-courses/basic-courses-application/

Preliminary course dates 2022:

19-20 September (in Uppsala)

26-27 October (Zoom)

15-16 November (in Uppsala)

Responsible department

Division of Planning, Lotta Jäderlund

Practical skills in sequence analysis, 2 ECTS (PNS0191)

Today basic knowledge of sequence analysis methods such as sequence homology searches and phylogenetic analysis is an essential skill set to complement wet lab experimental work within the life sciences. Fairly simple analyses of biological sequences can reveal a lot about gene function and lead to the formulation of new and unexpected hypotheses for experimental verification. This course will demonstrate to the students how basic methods in sequence analysis can improve their understanding of one or more target genes or proteins that are relevant to their PhD projects.

The course is aimed at PhD students whose main research focus is not bioinformatics but whose PhD projects involve biological sequences (e.g. biochemistry, genetics, molecular biology, cell biology, structural biology, microbiology). The course strives to improve the bioinformatic literacy of students, which will enable them to get to know their favorite gene(s) or protein(s) better, provide them with the necessary skills to evaluate these types of analyses in the published scientific literature as well as allow the students to generate novel hypotheses for future wet lab experiments.

The course will cover the fundamentals of sequence analysis including sequence databases, sequence homology searches, multiple sequence alignments, sequence motif searching and phylogenetic analysis. The course will also cover how to describe and visualize results of sequence analysis in an informative manner. The course will mainly rely on web-based tools. Note that the course will NOT cover any programming, genome assembly or analysis of genome-scale datasets (e.g. transcriptomics, proteomics, metagenomics). For more detailed information about course content and preliminary course dates, please see the syllabus and schedule attached.

The course is organized by Tomas Linder at the Department of Molecular Sciences on behalf of the SLU Organism Biology graduate school. The course will be held in English and conducted remotely via Zoom. The course can accommodate a maximum of 12 students.

To register for this course, send an e-mail to Tomas.Linder@slu.se specifying your name, department and position no later than October 15^th, 2022.

Link to syllabus

Link to scheduele

Thesis summary writing workshop

October 21st, 2022 at 9:15-14:30

at Loftet, Campus Ultuna, SLU and via Zoom.

Welcome to our thesis summary writing workshop for PhD students!

The aim of the workshop is to give insights and inspiration on how to

write a thesis summary. The topics covered are legal issues concerning

the thesis summary writing process, writing inspiration, and discussions

on “best practices” for writing a thesis summary.

Application and information

Register by email to philip.jacobson@slu.se on October 6th at the latest.

Please state your department and if you wish to attend at Ultuna or via

video (Zoom). If you wish to attend at Ultuna, please state allergies or

food preferences (vegetarian lunch and fika will be included). More

information and schedule can be found on the research school’s

homepage.

For further questions, please contact the workshop organizer:

Philip Jacobson

Dept. of Aquatic Resources

+46(0)10-478 42 78

philip.jacobson@slu.se

The workshop is jointly organized by The NJ-faculty Research Schools

Focus on Soils and Water, Ecology – basics and applications, Organism

Biology, Society and Landscape, Sustainable Systems for Food, Energy

and Biomaterials, and is open for all PhD students at SLU.

Program

Invitation

Real Time Quantitative PCR – theory, experimental design and data analysis, 3.5 ECTS (P000008)

Nov 29^th to Dec 19^th

Real-time quantitative PCR is a very popular method broadly used and miss-used in molecular biology. The aim of this course is not only to teach the very basics of the qPCR method, but also to introduce students to the MIQE guidelines essential for designing, performing and interpreting quantitative experiments in a reliable way. During the course we will go through ins and outs of the qPCR method and how it relates to other methods, such as NGS and microarrays. We will use tools for primer design, data normalization and analysis and discuss experimental setups. The course also includes a practical part, during which students will design their own experiments, design and order primers, prepare templates, perform qPCR and analyze the data. 

The course, organized and taught by Alyona Minina on behalf of the research school Organism Biology, will run from Nov 29^th to Dec 19^th 2022. Teaching will be carried out in the form of lectures and seminars combined with group works as well as lab work at Uppsala BioCenter. For more info about the content and format of the course, please see the course syllabus and tentative program attached.

The course can accommodate a maximum of 15 students and priority is given to SLU PhD students. To register for this course, please fill in this form:  https://forms.gle/VUu1oxSiw6Wd382a8 no later than Nov 11.

Link to syllabus

Link to scheduele

Spring 2022

Visualize your Science, 4 ECTS (PNG0073)

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake. 
 
The course is software independent and will cover things like use of colors, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know 

- How to create beautiful and credible scientific posters.

- How to use professional illustration software to illustrate your research.

- Where to find images, if you cannot draw them yourself.

- How to create images that are simple but yet informative.

The course runs on part time from March 1^st to May 13^th. For more info about the course, see the syllabus and the schedule attached. You can also visit the course home page at https://www.visualizeyourscience.com/pages/vys-course.

The course normally represents a mix of online theory and drawing tutorials complemented with four face-to-face sessions. Given the Covid-19 pandemic all joint sessions will be in form of on-line sessions this time.

The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see the short résumé attached.

The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For binding registration on first serve basis (student number limited to 20), send an e-mail before February 17^th to Katarina.Landberg@slu.se indicating your name, department and position. In principle, all costs for the course are covered by the research school Organism Biology. The one exception is if a registrant fail to attend the course without informing the organizer in due time. If this happens, the person must pay the actual course fee of 575€.  

Link to syllabus

Link to schedule

Link to résumé about organizer

Practical skills in sequence analysis, 2 ECTS (PNS0191)

Planned for spring 2022.

Today basic knowledge of sequence analysis methods such as sequence homology searches and phylogenetic analysis is an essential skill set to complement wet lab experimental work within the life sciences. Fairly simple analyses of biological sequences can reveal a lot about gene function and lead to the formulation of new and unexpected hypotheses for experimental verification. This course will demonstrate to the students how basic methods in sequence analysis can improve their understanding of one or more target genes or proteins that are relevant to their PhD projects.

The course is aimed at PhD students whose main research focus is not bioinformatics but whose PhD projects involve biological sequences (e.g. biochemistry, genetics, molecular biology, cell biology, structural biology, microbiology). The course strives to improve the bioinformatic literacy of students, which will enable them to get to know their favorite gene(s) or protein(s) better, provide them with the necessary skills to evaluate these types of analyses in the published scientific literature as well as allow the students to generate novel hypotheses for future wet lab experiments.

The course will cover the fundamentals of sequence analysis including sequence databases, sequence homology searches, multiple sequence alignments, sequence motif searching and phylogenetic analysis. The course will also cover how to describe and visualize results of sequence analysis in an informative manner. The course will mainly rely on web-based tools. Note that the course will NOT cover any programming, genome assembly or analysis of genome-scale datasets (e.g. transcriptomics, proteomics, metagenomics). For more detailed information about course content and preliminary course dates, please see the syllabus and schedule attached.

The course is organized by Tomas Linder at the Department of Molecular Sciences on behalf of the SLU Organism Biology graduate school. The course will be held in English and conducted remotely via Zoom. The course can accommodate a maximum of 12 students.

How to become a postdoc

Planned for spring 2022.

Welcome to a one-day workshop where you will meet representatives from the Swedish research councils Formas and VR, the union (SULF), and several post docs. We have also invited two researchers that will discuss and give you their perspectives on writing applications and evaluating applications.

Please contact the coordinator, Helena Bylund, for more information.

Thesis summary writing workshop

Planned for spring 2022.

Welcome to a one-day workshop about writing a thesis summary (Kappa).

Please contact the FoSW coordinator, Maria Kahlert, for more information.

Autumn 2021

”Picture a Scientist” – watch it now!

The SLU University Library has acquired a one-year licence for the movie “Picture a Scientist” (2020). The movie highlights gender inequality and equal opportunities in the academic world and is available to all staff members and students.

Gender equality and equal opportunities at SLU is a key fundament of our institution, and to raise awareness of these issues in a scientific context, the SLU University Library has acquired a one-year licence to the movie “Picture a Scientist” (2020).

The movie is described on www.filmplatform.net as follows:

“PICTURE A SCIENTIST is a feature-length documentary film chronicling the groundswell of researchers who are writing a new chapter for women scientists. A biologist, a chemist and a geologist lead viewers on a journey deep into their own experiences in the sciences, overcoming brutal harassment, institutional discrimination, and years of subtle slights to revolutionize the culture of science. From cramped laboratories to spectacular field sites, we also encounter scientific luminaries who provide new perspectives on how to make science itself more diverse, equitable, and open to all.”

The movie will be available until the 10th of May 2022 to all SLU staff members and students via the library catalogue (and through the SLU VPN):

• Picture a scientist in the library search service Primo

In collaboration with the SLU University Library as well as the NJ and VH faculties, The SLU Research School Organism Biology will host a panel discussion based on and around the movie and gender equality at Swedish Higher Education Institutions. This event will take place on 23rd September 2021. Stay tuned for more information!

For more information, please contact Eddy Vélëz.

Confocal Microscopy, 5 ECTS (PNS0138)

February 7^th – 18^th

The aim of this course is to provide students with a solid theoretical background essential for designing confocal microscopy experiments, introductions to common softwares used in the area and also to give students hands-on experience with confocal microscopes available at the BioCenter. For information about the course schedule and syllabus, see links below. Number of participants limited to 16. PhD students will be given priority. To register for the course, send an e-mail to Adrian Dauphinee, no later than January 13th, 2022.

Course Syllabus

Course Schedule

Visualize your Science, 4 ECTS (PNG0073)

Sept 21^st to Nov 26^th.

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake. 
 
The course is software independent and will cover things like use of colors, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know 

- How to create beautiful and credible scientific posters.

- How to use professional illustration software to illustrate your research.

- Where to find images, if you cannot draw them yourself.

- How to create images that are simple but yet informative.

The course runs on part time from Sept 21^st to Nov 26^th. For more info about the course, see links to the syllabus and the schedule below. You can also visit the course home page at https://www.visualizeyourscience.com/pages/vys-course.

The course normally represents a mix of online theory and drawing tutorials complemented with four face-to-face sessions. Given the Covid-19 pandemic all joint sessions will be in form of on-line sessions this time.

The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see link to short résumé below.

The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For binding registration on first serve basis (student number limited to 20), send an e-mail before Sept 15^th to Mattias.Thelander@slu.se indicating your name, department and position. In principle, all costs for the course are covered by the research school Organism Biology. The one exception is if a registrant fail to attend the course without informing the organizer in due time. If this happens, the person must pay the actual course fee of 575€.  

Link to syllabus

Link to schedule

Link to résumé about organizer

Multivariate methods for ecologists, 3 ECTS or 4.5 ECTS (PNS0190; PNS0074)

25 October to 12 November 2021

The course aims to illustrate the application of a number of multivariate methods on ecological data. Following the course, participants should be familiar with different multivariate techniques, and how they can be applied on various types of data. The course will focus on developing an understanding of the application of multivariate techniques, with only a minimum amount of effort placed on comprehending the underlying mathematical detail.

Applications

The course is given in two parts. The first part (one week) is compulsory and consists of lectures and exercises. The second part is optional and consists of two weeks of supervised work with own data. The course will also in 2021 be entirely on-line.

An invitation will be sent out in late August 2021. We do not accept applications before the invitation is sent, but we can put interested students on the send list (e-mail Sara Sandström).

More details at the Department of Aquatic Sciences and Assessment.

For more information, please contact:

Ulf Grandin (course content etc.)

Sara Sandström (application, practical matters, etc.)

Understanding and coding the R language, 2 ECTS

The aim of the course is to help each student overcome the initial steep learning curve that is associated with learning R, and how to think in a structured and logical way to make programming easier.

• November
• 2 ECTS
• PNG008
• Organizers: Matt Low, RS Ecology, FoSW and Organism Biology.
• Apply no later than 1 October.
• More information and application form.

PhDs Careers Outside Academia

Do you want to pursue a career outside of academia?!  Have you asked yourself what possibilities you, as a PhD, have in the labour market outside of the university?!

Do you want to improve your chances of finding your dream job?!!

Then come to the one-day seminar hosted by the NJ-faculty research schools to hear from former PhD students that graduated and have gone on to pursue jobs outside the university setting.  You will get a different perspective on careers choices, finding your “dream job”, self-employment possibilities, prospects and possibilities in the current labour market, etc.

The workshop is jointly organized by Focus on Soils and Water, Organism Biology, Ecology –basics and applications, Focus on Food and Biomaterials, Social Science Perspective on Sustainable Development, Society and Landscape, Sustainable Biomass Systems -- Magdalena Bieroza & Eddy Vélëz

Actual dates will be announced shortly.  Send an email to Eddy Vélëz for more information.

Mycology – its basics and applications (4 ECTS)

November 29 - Dec 6, 2021

This six-day course aims to provide students with basic mycological concepts (e.g., taxonomy, physiology, genomics, etc.) as well as in-depth research examples in the form of lectures within selected areas of mycology. The course is open to PhD students and other interested scientists.

The course consists of preparatory literature reading (review articles), lectures, discussions, and a final oral presentation. The basic concepts will be complemented by in-depth research examples from SLU scientists and keynote speakers from other research institutions in Sweden and abroad. Active participation by the students is required. At the end of the course, the students will deliver an oral presentation in which they will discuss what they have learned during the course and how it could be applied or is relevant to their own research projects.

For further information about the course, see the attached syllabus. If there are additional questions, don't hesitate to contact the course leaders Marisol Sánchez-García and Georgios Tzelepis at the department of Forest Mycology and Plant Pathology.

To register for the course, send an e-mail to Marisol Sánchez-García or Georgios Tzelepis no later than November 19th, 2021.

The course will be given through zoom and in a classroom at BioCentrum.

Syllabus

Schedule

Advances in Enzyme Regulation (5 ECTS)

The course will focus on recent advances in chemical biology, with emphasis on enzyme regulation. You will learn about drug design and high-throughput screening, single-molecule imaging and cryo-electron microscopy, guided nanomolecular assemblies and enzyme engineering, N-terminomics and discovery of intrinsically disordered proteins. The program includes two modules: lectures on above topics delivered by world leading experts and training in writing research proposals.

Actual dates will be announced shortly.  Send an email to Eddy Vélëz for more information.

Analysis of High Throughput Sequencing RNA-Seq Data

(November 29 ^th-30^th); December 6^th - December 10^th; (December 17^th)

High Throughput Sequencing (HTS) technologies and in particular Next Generation Sequencing (NGS) have revolutionized the way we conduct gene expression analysis. In comparison to micro-array-based methods, NGS has unleashed an almost unlimited power to perform gene expression analysis, for a similar price and with faster, more comprehensive, more efficient and more reproducible characteristics. Rapidly, the data generation rate has exceeded the analytical capabilities and data analysis has become the major bottleneck in gene expression studies.

The SLU Bioinformatics Infrastructure (SLUBI) is organizing an advanced course for the Organism Biology Research School, aimed at PhD students, that has the objective to help addressing this problem by (i) helping participants critically assess the challenges faced in the HTS field, (ii) developing efficient communication skill with bioinformatician, and (iii) training students in analyzing HTS data. For detailed info about the course, please see the syllabus and preliminary schedule attached.

The aims of this course are to:

• familiarize the participants with advanced RNA-Seq data analysis methodologies and how biological knowledge can be gained from these by illustrating different analyses approaches
• allow the participants to acquire computational competences about latest RNA-Seq analytical approaches and related statistical methods
• expose the participants to modern computing technologies, as the computer hands-on of the course will be performed using cloud computing resources
• develop the participants’ awareness to critically reflect onto RNA-Seq analysis strengths and weaknesses
• enable participants to perform the analysis of their own data (in stance of the exemplary dataset otherwise available)

The course has one main module, and two optional modules (two and one ECTs credits each, respectively). The main module covers the analysis of RNA-Seq data, while the first optional module is an introduction to the Unix and R environments to give attendees the necessary admission requirements for the main module. The second optional module is a follow-up for attendees to apply the knowledge gained from the main module content on their own data. The course will provide two to four ECTS credits depending on the selected modules, as follows:

Module 1 (optional) 2 days - 1 ECTS

Module 2 (mandatory) 5 days - 2 ECTS

Module 3 (optional) 1 day - 1 ECTS

The course will be conducted online only. However, if students wish so, they can organise themselves in groups and join using one of the teaching facilities available at SLU.

The course has a maximum number of participants is 20. PhD students will be prioritised, but admission will be on a first-come, first-served basis, provided that the minimal requirements are met. Application deadline: Nov 12. To register, follow this link: https://forms.gle/wEK6DCz47UcPX1Ya9.

If you have any question, please contact the course leaders (nicolas.delhomme@slu.se, amrei.binzer-panchal@slu.se) or the slack channel #organism-biology-research-school-rna-seq-course of the slubi-workspace.slack.com workspace.

Syllabus

Preliminary course schedule

Spring 2021

Visualize your Science, 4 ECTS (PNG0073)

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake. 
 
The course is software independent and will cover things like use of colors, text and typography, signs and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know 

- How to create beautiful and credible scientific posters.

- How to use professional illustration software to illustrate your research.

- Where to find images, if you cannot draw them yourself.

- How to create images that are simple but yet informative.

The course runs on part time from March 2 to May 7. For more info about the course, see links to the syllabus and the schedule below. You can also visit the course home page at https://www.visualizeyourscience.com/pages/vys-course.

The course normally represents a mix of online theory and drawing tutorials complemented with four face-to-face sessions. Given the Covid-19 pandemic all joint sessions will be in form of on-line sessions this time.

The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see link to short résumé below.

The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For binding registration on first serve basis (student number limited to 20), send an e-mail before February 24 to Mattias Thelander indicating your name, department and position. In principle, all costs for the course are covered by the research school Organism Biology. The one exception is if a registrant fail to attend the course without informing the organizer in due time. If this happens, the person must pay the actual course fee of 575€.   

Link to syllabus

Link to schedule

Link to résumé about organizer

Practical skills in sequence analysis, 2 ECTS (PNS0191)

March 17^th to April 14^th, 2021.

Today basic knowledge of sequence analysis methods such as sequence homology searches and phylogenetic analysis is an essential skill set to complement wet lab experimental work within the life sciences. Fairly simple analyses of biological sequences can reveal a lot about gene function and lead to the formulation of new and unexpected hypotheses for experimental verification. This course will demonstrate to the students how basic methods in sequence analysis can improve their understanding of one or more target genes or proteins that are relevant to their PhD projects.

The course is aimed at PhD students whose main research focus is not bioinformatics but whose PhD projects involve biological sequences (e.g. biochemistry, genetics, molecular biology, cell biology, structural biology, microbiology). The course strives to improve the bioinformatic literacy of students, which will enable them to get to know their favorite gene(s) or protein(s) better, provide them with the necessary skills to evaluate these types of analyses in the published scientific literature as well as allow the students to generate novel hypotheses for future wet lab experiments.

The course will cover the fundamentals of sequence analysis including sequence databases, sequence homology searches, multiple sequence alignments, sequence motif searching and phylogenetic analysis. The course will also cover how to describe and visualize results of sequence analysis in an informative manner. The course will mainly rely on web-based tools. Note that the course will NOT cover any programming, genome assembly or analysis of genome-scale datasets (e.g. transcriptomics, proteomics, metagenomics). For more detailed information about course content and preliminary course dates, please see the syllabus and schedule attached.

The course is organized by Tomas Linder at the Department of Molecular Sciences on behalf of the SLU Organism Biology graduate school. The course will be held in English and conducted remotely via Zoom. The course can accommodate a maximum of 12 students.

To register for this course, send an e-mail to Tomas Linder specifying your name, department and position no later than March 3, 2021.

Course Syllabus

Tentative course schedule

How to become a postdoc

Planned for Spring 2021.

Welcome to a one-day workshop where you will meet representatives from the Swedish research councils Formas and VR, the union (SULF), and several post docs. We have also invited two researchers that will discuss and give you their perspectives on writing applications and evaluating applications.

Please contact the coordinator, Helena Bylund, for more information.

Thesis summary writing workshop

Spring 2021.

Welcome to a one-day workshop about writing a thesis summary (Kappa).

Please contact the FoSW coordinator, Maria Kahlert, for more information.

How to write and publish a scientific paper (4.5 HEC)

March 10^th – June 16^th, 2021, via Zoom.

Scientific writing is an acquired skill that can be learned. This course provides instructions on how to structure and format each section of a scientific manuscript according to the IMRAD format, based on the book ‘Writing Scientific Research Articles: Strategy and Steps’ by Margaret Cargill & Patrick O’Connor (2009). Focus is placed on basic writing skills, particularly on how to write clear and concise sentences, paragraphs and sections. We will also discuss how to best present data in figures, how to use references and how reference software can be useful.

The students work on their own manuscripts throughout the course, integrating theory and practice. Thus, it is imperative that the students are at a writing stage in their research. Constructive feedback and analysis of these texts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a manuscript ready for submission. The course will also include additional exercises and analysis of already published material.

The course will commence on Wed March 10th from 10am-12, and then every two weeks until June 16th. Scheduled activities are eight group-sessions (2h) approximately every two to three weeks. Additional studies (not scheduled) consist of literature studies and written exercises.

The number of participants is limited to 10. Priority will be given to members of the Organism Biology and Focus on Soils and Waters research schools, but is open also to other PhD students.

For registration and more information, send an email to the course organizer, Marisol Sanchez-Garcia no later than March 2nd 2021.

Real Time Quantitative PCR – theory, experimental design and data analysis (3.5 ECTS, PNS0215)

Real-time quantitative PCR is a very popular method broadly used and miss-used in molecular biology. The aim of this course is not only to teach the very basics of the qPCR method, but also to introduce students to the MIQE guidelines essential for designing, performing and interpreting quantitative experiments in a reliable way. During the course we will go through ins and outs of the qPCR method and how it relates to other methods, such as NGS and microarrays. We will use tools for primer design, data normalization and analysis and discuss experimental setups. The students will perform analysis of provided qPCR data and will be encouraged to test their new skills on the data of their interest.

The course, organized and taught by Alyona Minina on behalf of the research school Organism Biology, will run from April 15th to 30th. The course will be conducted remotely via Zoom and will not include wet lab work, meaning that it will be compatible with social distancing rules that may be in place at the time. For more info about the content and format of the course, please see links to the course syllabus and program below.

The course can accommodate a maximum of 16 students and priority is given to SLU PhD students. To register for this course, send an e-mail to Mattias Thelander specifying your name, department and position no later than March 25, 2021.

Syllabus (PNS0215)

Program (PNS0215)

Pathobiome and Plant Immunity (PFG0079: 5 credits or PFG0080: 2 Credits)

A new PhD course, ‘Pathobiome and Plant Immunity’, will be offered via Zoom from June 7th to the 16^th.  The course will provide students with the opportunity to understand emerging concepts in the field of plant-microbe interactions based on the study of pathogen-pathogen, pathogen-microbiome, and plant-microbiome interactions, with a particular focus on crops.

We were fortunate enough to attract internationally leading experts in the field, to whom we are very grateful (list in chronological order):

Monica Höfte. Ghent University (Belgium)

Maggie Wagner. University of Kansas (United States)

Bart Thomma. University of Cologne (Germany) - Keynote

Marie-Hélène Balesdent. INRAe (France)

Jiasui Zhan. SLU – Uppsala (Sweden)

Sophien Kamoun. The Sainsbury Laboratory (United Kingdom) - Keynote

Laura Grenville-Briggs Didymus. SLU – Alnarp (Sweden)

Cara Haney. University of British Columbia (Canada) - Keynote

Daniel Croll. University of Neuchâtel (Switzerland)

Britt Koskella. University of California Berkeley (United States) - Keynote

Christine Faulkner. John Innes Centre (United Kingdom)

Full-time (PFG0079; 5 credits- min 12, max 20 students) and Part-time (PFG0080; 2 credits – not-limited) registrations for students are being offered.

Early registration deadline is April 2, 2021 (Both full- and part-time registrations are accepted. Full-time registrations will be prioritized).

Late registration deadline is April 30, 2021 (Part-time registrations are accepted. Full-time registrations will be offered if the limit of 20 students is not reached).

Please download, fill out the registration form, and send it to the course leader by email to Salim Bourras

Registration Form

Syllabus

Program

Genome editing by CRISPR/Cas9 in theory and practice, (5 credits, PNS0151)

The SLU research school Organism Biology welcomes PhD students and other interested scientists to a course in genome editing (5 credits). Gene-editing technologies such as CRISPR already transform science at an astonishingly rapid rate (Nobel Prize in 2020 in Chemistry). In this course we will cover the basics of genome editing and guide you through genome editing workflows, with laboratory instruction. Due to the pandemic, the entire course will be conducted on-line via Zoom.

The course will take place on part time in May and will include lectures both from in-house scientists and well-renowned international experts. The course is organized by Panagiotis Moschou with help from Anna Törnkvist at the department of Plant Biology and invited speakers are Florian Veillet (INRAE, France) and Thomas Jacobs (VIB, Belgium). For more detailed information about the course, please refer to the course syllabus and the preliminary schedule linked to below.

For registration on first serve basis (student number limited to 20), send an e-mail before March 22 to panagiotis.moschou@slu.se indicating your name, university, department and position.

Course syllabus

Course schedule

From population to ecological functional genomics: Concepts, tools and applications (2.5 ECTS; PNS0221)

Next generation sequencing has revolutionized evolutionary biology allowing unprecedented accumulation of data that help yield insights into evolutionary questions that were unapproachable only a few years ago. This course will provide an introduction to basic population genomic analysis using single nucleotide polymorphism (SNP) data and focus one key analysis methods required to successfully analyze a population genetic data set. The course will NOT cover steps prior to the generation of a SNP data set, such as NGS data processing and SNP calling. The course will provide a brief introduction to Linux and the command line environment, including file conversions, manipulation and job management on HPC clusters. The main topics of the course are analyses of population structure and differentiation, demographic history inference, analysis of admixture and introgression, the genomic basis of adaptive evolution and ecological functional genomics. Having completed the course, students should have a good understanding of the software and methods available for population genomic analysis and be competent in basic population genomic analyses.

The course is aimed at PhD students who are interested in using population genomic analyses in their research projects. No previous experience of bioinformatics is required, but basic knowledge of evolutionary biology and population genetics concepts are desirable. The course will use a range of software, including the Linux operating system and use of high-performance computing clusters.

The course is organized by Pär Ingvarsson and Adrien Sicard at the Department of Plant Biology on behalf of the SLU Organism Biology graduate school (OB). The course will be held in English and conducted remotely via Zoom. The course can accommodate a maximum of 15 students. For more detailed information about the course, please see links to the syllabus and the schedule below.

To register for this course, send an e-mail to Pär Ingvarsson specifying your name, department and position no later than April 23rd, 2021.

Course Syllabus

Course Schedule

Visualize your Science, 4 ECTS (PNG0073)

September 22 - November 27, 2020

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighbouring fellow posters and presentations that keep your audience awake.

The course is software independent and will cover things like use of colours, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know:

- How to create beautiful and credible scientific posters.

- How to use professional illustration software to illustrate your research.

- Where to find images, if you cannot draw them yourself.

- How to create images that are simple but yet informative.

The course runs on part time from September 22 to November 27. For more info about the course, see the syllabus and the schedule attached. You can also visit the course home page at https://www.visualizeyourscience.com/pages/vys-course.

The course normally represents a mix of online theory and drawing tutorials complemented with four face-to-face sessions. Given the Covid-19 pandemic the introductory joint session on October 8 will be in form of an on-line lecture this time. Depending on how the pandemic evolves also subsequent joint sessions may be changed from face-to-face to on-line events. In case face-to-face sessions will be offered at all participants may still choose to join via link if they prefer.  

The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see the short résumé attached.

The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For binding registration on first serve basis (student number limited to 20), send an e-mail before September 15 to Mattias.Thelander@slu.se indicating your name, department and position. In principle, all costs for the course are covered by the research school Organism Biology. The one exception is if a registrant fail to attend the course without informing the organizer in due time. If this happens, the person must pay the actual course fee of 575€.

Course Syllabus

Time and Place for face-to-face sessions

About the course organizer

Root-soil-microbe interactions

October 12 - 16, 2020

Interactions involving plant roots and microbes may be beneficial (e.g. symbiotic associations) or pathogenic in their nature. This course focuses on beneficial root-soil-microbe interactions in the rhizosphere of both agricultural and forest ecosystems. You will learn about fundamental concepts concerning e.g. rhizosphere, nitrogen-fixing root nodule symbioses, mycorrhizal symbiosis, soil bacteria and archaea. As well as gain a solid understanding of how microorganisms interact with plant roots and the surrounding soil.  One focus will be on the roles that microorganisms have in nutrient and carbon cycling, as well as their role in plant protection and sustainable agriculture. The course will also cover commonly used methods to study root-soil-microbe interactions.

CONTENT:  The course consists of one intense week of full-time studies preceded by individual literature studies of selected scientific papers. The scheduled course week includes lectures by invited national and international teachers, literature discussions and PhD student presentations. The lectures will be open for all interested students/researchers.

ADDITIONAL INFORMATION:  This course is given as a postgraduate course within the SLU Research School Organism Biology in Uppsala, Sweden.  The course will be offered via Zoom during week 42, 12-16th of October, preceded by individual literature studies.

For more information and registration, please contact Petra Fransson.

Multivariate methods for ecologists, (PNS0190 or PNS0074)

November 2 - 27, 2020

The course aims to illustrate the application of a number of multivariate methods on ecological data. Following the course, participants should be familiar with different multivariate techniques, and how they can be applied on various types of data. The course will focus on developing an understanding of the application of multivariate techniques, with only a minimum amount of effort placed on comprehending the underlying mathematical detail.

• The course is given in two parts. The first part (2-6 November 2020) is compulsory and consists of lectures and exercises.
• The second part (9-20 November) is optional and consists of supervised work with own data, at your home university.
• Due to the Corona pandemic, the 2020 course will be entirely on-line.
• Course organizer: Ulf Grandin, Department of Aquatic Sciences and Assessment.
• Course code: For 3 ECTS PNS0190 and for 4.5 ECTS PNS0074.

Applications

Applications should be sent by e-mail to Sara Sandström. The application should contain:

• Name
• Personnummer/Civil registration number
• Affiliation (including post address)
• Will take only Part 1 or the Full course (see below)
• A pdf (or corresponding) of a certificate stating that you are a PhD student.

There are a limited number of places at the course. Attendants will be accepted in the order we receive the applications, i.e. first come, first served!

Last day for application is 30 September 2020.

Post Doc researchers may attend the lectures if there is room. Send a corresponding application, but tell that you are a post doc researcher!

More details at the Department of Aquatic Sciences and Assessment.

For more information, please contact:

• Ulf Grandin (course content etc.), e-mail: ulf.grandin@slu.se
• Sara Sandström (application, practical matters, etc.), e-mail: sara.sandstrom@slu.se

Seminar:  Academic productivity& Stress handling

When:  November 6th, 2020.       Where:  Room V in Ulls Hus, SLU Ultuna

Workshop by “Finish on time”: 

“As individuals, we often have a main strategy, or a certain way of thinking and acting, that we use in a variety of situations. Often our main strategy works well, but when we face new situations, we may need a wider range or variety of strategies. This conference is thus aimed at providing you with new strategies that are applicable to your work situation. We will cover productivity tools about setting and evaluating goals as well as a matrix for prioritizing between tasks. We combine these tools with stress management and answer questions such as:  What is stress? What factors explains stress in the academic environment? What are automatic thoughts, with common themes such as perfection and the impostor syndrome, and how do they affect me? Which strategy is most useful for managing my automatic thoughts?”

Theory is combined with practical exercises in smaller groups during the conference.  This IRL event is limited to 30 students!!

  9.00                 Introduction and 80/20 including exercise (two and two discussion)

10.00                 Coffee break

10.15                 End product focus and SMART goals

11.00                 Stress in academia: Definition of stress and exercise about the demand-control-support model (groups of two doing an exercise on a matrix on the floor)

12.00                 Lunchbreak

13.15                 Working in units (individual exercise)

14.00                 Stress and recovery (individual reflection task)

14.30                 Coffee break

15.00                 Coping strategies OR Feedback principles (Discussion among the participants)

15.30                 Summary and conclusion (each participants write down a short key take-away from the day and presents it to the others)

16.00                 End

To register, send an email to Eddy Vélëz as soon as possible, but before the 30th of October 2020. Please state department and allergies or food preferences.

You must be a member of the SLU Organism Biology Research School

Plant Disease Epidemiology– From Theory to Applications

December 7th to the 11th, 2020 via Zoom

The course aims to provide students opportunity to understand concepts, principles, state-of-the-art methodology, and research orientations within the area of plant disease epidemiology. After the course, the students should have reached a higher standard of applying available tools to study epidemiological processes and manage plant diseases. The course will also offer the students opportunities of linking to the research community within the area.

The course is organized into four topics ranging from principles, concepts and methodology of plant disease epidemiology to population genetics of plant pathogens, disease ecology and disease mitigations in agricultural, forestry or natural ecosystem. The principle, concepts and methodology will be complemented by in-depth research examples from an international team of scientists working in fundamental and applied research. The student will be required to read selected literature before and during the course period.

The following mandatory activities are require for successful completion of the course: i) active participation in the lecture and discussion of the entire course; ii) write a two-page report on what the student has learned during the course; and iii) write a description (1-2 pages) on how the concepts and technologies outlined in the course are related to the students’ field of research.

For further information about the course or to register, send an e-mail to Prof Jiasui Zhan no later than November 20, 2020.

Course syllabus

Course schedule

Analysis of High Throughput Sequencing RNA-Seq Data

(Nov 23-24); Nov 30 - Dec 4; (Dec 10)

High Throughput Sequencing (HTS) technologies and in particular Next Generation Sequencing (NGS) have revolutionized the way we conduct gene expression analysis. In comparison to micro-array-based methods, NGS has unleashed an almost unlimited power to perform gene expression analysis, for a similar price and with faster, more comprehensive, more efficient and more reproducible characteristics. Rapidly, the data generation rate has exceeded the analytical capabilities and data analysis has become the major bottleneck in gene expression studies.

The SLU Bioinformatics Infrastructure (SLUBI) is organizing an advanced course for the Organism Biology Research School, aimed at PhD students, which has the objective to help addressing this problem by (i) helping participants critically assess the challenges faced in the HTS field, (ii) developing efficient communication skill with bioinformatician, and (iii) training students in analyzing HTS data. For detailed info about the course, please see the syllabus and schedule attached.

The aims of this course are to:

• familiarize the participants with advanced RNA-Seq data analysis methodologies and how biological knowledge can be gained from these by illustrating different analyses approaches
• allow the participants to acquire computational competences about latest RNA-Seq analytical approaches and related statistical methods
• expose the participants to modern computing technologies, as the computer hands-on of the course will be performed using cloud computing resources
• develop the participants’ awareness to critically reflect onto RNA-Seq analysis strengths and weaknesses
• enable participants to perform the analysis of their own data (in stance of the exemplary dataset otherwise available)

The course has one main module, and two optional modules (two and one ECTs credits each, respectively). The main module covers the analysis of RNA-Seq data, while the first optional module is an introduction to the Unix and R environments to give attendees the necessary admission requirements for the main module. The second optional module is a follow-up for attendees to apply the knowledge gained from the main module content on their own data. The course will provide two to four ECTS credits depending on the selected modules, as follows:

• Module 1 (optional) 2 days - 1 ECTS
• Module 2 (mandatory) 5 days - 2 ECTS
• Module 3 (optional) 1 day - 1 ECTS

Due to the current COVID-19 situation, the course will be conducted online only. However, if students wish so, they can organise themselves in groups and join using one of the teaching facilities available at SLU.

The course has a maximum number of participants is 20. PhD students will be prioritised, but admission will be on a first-come, first-served basis, provided that the minimal requirements are met. To register, follow this link: https://forms.gle/ER3ZE2g7JpBheD11A. Application deadline: Nov 9.

If you have any question, please contact the course leader (nicolas.delhomme@slu.se) or the slack channel #organism-biology-research-school-rna-seq-course of the slubi-workspace.slack.com workspace.

Course syllabus

Course schedule

PhDs Careers Outside Academia

December 1^st, 2020 via Zoom!

Do you want to pursue a career outside of academia?!  Have you asked yourself what possibilities you, as a PhD, have in the labour market outside of the university?!

Do you want to improve your chances of finding your dream job?!!

Then come to the one-day seminar hosted by the NJ-faculty research schools to hear from former PhD students that graduated and have gone on to pursue jobs outside the university setting.  You will get a different perspective on careers choices, finding your “dream job”, self-employment possibilities, prospects and possibilities in the current labour market, etc.

Programme:

10.00 – 11.00 Job coach, Per Edenhamn and Dagrun Ellmer, Career Services at SLU

11.00 – 11.20 Hadden Graham, Foliumscience

11.20 – 11.40 Liza Ilskog, 2050 Consulting

11.40 – 12.00 Lars-Johan Larsson, Pharmacia/Amersham/GE Healtcare

12.00 – 13.00 Lunch break

13.00 – 13.20 Maria Tunberg, Analysys Mason

13.20 – 13.40 Anna Malmström, Swedish Energy Agency

13.40 – 14.00 Johanna Jansson, Jordbruksverket

14.00 – 14.20 Agnes Willén, Naturvårdsverket (Swedish EPA)

14.20 – 14.40 Karin Bennmarker, SLU Alumni

To register:  Send an email to Eddy as soon as possible, but before the 27th of November 2020. Please state your department name.

The workshop is jointly organized by Focus on Soils and Water, Organism Biology, Ecology –basics and applications, Focus on Food and Biomaterials, Social Science Perspective on Sustainable Development, Society and Landscape, Sustainable Biomass Systems -- Magdalena Bieroza & Eddy Vélëz

Special thanks to the SLU Alumni Network! 

Join the Alumni Network!! For information, please visit the following links:

https://www.slu.se/en/collaboration/slu-alumni/ 

https://www.slu.se/en/collaboration/slu-alumni/join-the-slu-alumni-network/

Understanding and coding the R language, 2 ECTS

Planned for April-May 2020.
This course provides basic knowledge in the R programming language and tools for programming, processing data and analyses. For more information, please contact the course organizer Matt Low.

Root-soil-microbe interactions, 3.5 ECTS (PNS0078)

April 20-24, 2020

Interactions involving plant roots and microbes may be beneficial (e.g. symbiotic associations) or pathogenic in their nature. This course focuses on beneficial root-soil-microbe interactions in the rhizosphere of both agricultural and forest ecosystems. You will learn about fundamental concepts concerning e.g. rhizosphere, nitrogen-fixing root nodule symbioses, mycorrhizal symbiosis, soil bacteria and archaea. As well as gain a solid understanding of how microorganisms interact with plant roots and the surrounding soil.
One focus will be on the roles that microorganisms have in nutrient and carbon cycling, as well as their role in plant protection and sustainable agriculture. The course will also cover commonly used methods to study root-soil-microbe interactions.
Please contact Petra Fransson for more information.

To communicate science, 2 ECTS (POG0084)

March 10-12 + April 28-29, 2020

Interaction with the society is becoming more and more important for researchers. To spread new knowledge and facilitate its usefulness is an important task for researchers and the universities, and it is also a prerequisite for getting research grants. This course teaches how to plan and perform communication work and what measures and channels that can be used to reach different target groups.

During the course different channels for research communication of popular science will be presented. Examples are poster presentation, press release and popular science writing, blogging, electronic and social media. This will be performed by lectures, seminars and practical exercises.
 
You can find the syllabus of the course via this link: https://www.slu.se/utbildning/program-kurser/kurser/?sprak=en&anmkod=P0059.1920
 
To sign up, please follow this link:
https://internt.slu.se/en/support-services/education/doctoral-education1/doctoral-courses/basic-courses-application/
The number of participants is limited to 15.
 
This course is organized in collaboration with all NJ research schools and the Division of Planning. If you have any questions please contact course organizer Lotta Jäderlund from the Division of Planning or send an e-mail to Elisabeth Müllner from the research school Focus on Food and Biomaterials.

How to become a postdoc

Planned for March 2020.
Welcome to a one-day workshop where you will meet representatives from the Swedish research councils Formas and VR, the union (SULF), and several post docs. We have also invited two researchers that will discuss and give you their perspectives on writing applications and evaluating applications.
Please contact coordinator Helena Bylund for more information.

Reviewing and Summarizing Science - Everything You Always Wanted to Know About Science* (*But Were Afraid to Ask), 2 ECTS (PNS0070)

March 16-20, 2020

The objective of the course are to help the students understand how to navigate
scientific publications and the process of scientific communication.
The course will teach you how to find and evaluate scientific key publications and to understand the purpose of the peer review system. You will learn how to write a constructive scientific review, but also how to summarize the key findings of a paper in 1-2 sentences, and to use conferences to your advantage.
Teacher: Antonia Liess, Lecturer, Högskolan i Halmstad. Please contact course coordinator Maria Kahlert for more information.

Thesis summary writing workshop

5 March 2020

Welcome to a one-day workshop about writing a thesis summary (Kappa).
Please contact FoSW coordinator Maria Kahlert for more information.

Practical skills in sequence analysis, 2 ECTS (PNS0191)

Jan 27-28 + Feb 6, 13, 19, 2020

Today basic knowledge of sequence analysis methods such as sequence homology searches and phylogenetic analysis is an essential skill set to complement wet lab experimental work within the life sciences. Fairly simple analyses of biological sequences can reveal a lot about gene function and lead to the formulation of new and unexpected hypotheses for experimental verification. This course will demonstrate to the students how basic methods in sequence analysis can improve their understanding of one or more target genes or proteins that are relevant to their PhD projects.
 
The course is aimed at PhD students whose main research focus is not bioinformatics but whose PhD projects involve biological sequences (e.g. biochemistry, genetics, molecular biology, cell biology, structural biology, microbiology). The course strives to improve the bioinformatic literacy of students, which will enable them to get to know their favorite gene(s) or protein(s) better, provide them with the necessary skills to evaluate these types of analyses in the published scientific literature as well as allow the students to generate novel hypotheses for future wet lab experiments.
 
The course will cover the fundamentals of sequence analysis including sequence databases, sequence homology searches, multiple sequence alignments, sequence motif searching and phylogenetic analysis. The course will also cover how to describe and visualize results of sequence analysis in an informative manner. The course will mainly rely on web-based tools. Note that the course will NOT cover any programming, genome assembly or analysis of genome-scale datasets (e.g. transcriptomics, proteomics, metagenomics). For more detailed information about course content and preliminary course dates, please see the syllabus and schedule attached.
 
The course is organized by Tomas Linder at the department of Molecular Sciences on behalf of the SLU Organism Biology graduate school. The course will be held in English at the Uppsala Biocenter and can accommodate a maximum of 12 students.
 
To register for this course, send an e-mail to Tomas Linder specifying your name, department and position no later than Dec 20, 2019.

Forest Pathology in the 21st century, 3 ECTS

18-22nd November 2019

The course will focus on the ecology of pathogens and damages to trees and forest ecosystems caused by forest pathogens. The course will cover aetiology of common forest pathogens globally e.g. Heterobasidion, Diplodia and Phytophthora spp., but also principles for population dynamics and factors of significance for pathogenicity and aggressiveness, such as climate impact and how introduced organisms can affect the stability of forest ecosystems.
The course will deal with research and key methods in the field, resistance biology in trees, molecular tools for identification of species and population structure analyses and Pest Risk Assessment.
The course organizer is Jan Stenlid (Dept. of Forest Mycology and Plant Pathology) and teachers will include researchers from SLU as well as invited top scientists in the field. The course will include lectures, computer simulations, laboratory exercise, and own assignments for each student and will be held full-time from 18-22 November 2019 at Ultuna campus.
For registration, more information, and questions, please contact Jan Stenlid (jan.stenlid@slu.se).

Basics of metagenomics analysis, 3 ECTS

11-15th November 2019

This course will cover the basics of metagenomics analysis of shotgun sequencing data. It will start with a brief overview over experimental design and introduction to DNA extraction and library construction for metagenomics projects. In the following the course will cover the bioinformatics analysis of metagenomics data, including data standards and submission, processing of raw data, assembly, functional and taxonomic annotation, overview of databases, retrieval and analysis tools. We will also discuss some of the pros and cons of metagenomics methods.
The course will include seminars, lectures and tutorials, and will take place 11-15 November 2019 at Ultuna campus in Uppsala. Teachers will include researchers from SLU, staff from the SLU bioinformatics infrastructure (SLUBI), as well as invited guest lecturers.
Basic knowledge of R and working on a command line is a prerequisite, because it would be difficult to follow the computer exercises otherwise. For that, the students are expected to complete a tutorial(s) regarding working in unix/linux/R environment prior to the course. Students will also get an assignment after the course that needs to be completed in order to receive the course credits. Participants need to bring their own laptops for the tutorials.
For registration and more information please contact the course organizer Sari Peura (sari.peura@slu.se). Note that places will be limited to 20. Registration deadline is October 20, 2019.

Visualize your Science, 4 ECTS (PNG0073)

Sep 17 – Nov 21, 2019

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake. 
 
The course is software independent and will cover things like use of colors, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice. 

After the course, you will know 
- How to create beautiful and credible scientific posters.
- How to use professional illustration software to illustrate your research.
- Where to find images, if you cannot draw them yourself.
- How to create images that are simple but yet informative. 

The course runs on part time from September 17 to November 21. It represents a mix of online theory and drawing tutorials and face-to-face feedback sessions. 

 For more info about the course, see the syllabus and the schedule attached. You can also visit the course home page at https://www.visualizeyourscience.com/pages/vys-course. The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see the short résumé attached.

The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For binding registration on first serve basis (student number limited to 20), send an e-mail before September 15 to Mattias.Thelander@slu.se indicating your name, department and position. In principle, all costs for the course are covered by the research school Organism Biology. The one exception is if a registrant fail to attend the course without informing the organizer in due time. If this happens, the person must pay the actual course fee of 575€. 

Course Syllabus

Time and Place for face-to-face sessions

About the course organizer

10th Annual Organism Biology Workshop: Apply for your future - Jobs, grants, CVs and interviews, 1ECTS

18-19 June 2019

This year’s annual workshop will focus on different types of applications and we will discuss how to prepare cover letters, grant proposals, interviews and CVs. The workshop will combine lectures from invited guests working within and outside of academia, and activities that will give you the chance to practise interview situations and get feedback on your CV. Active participation in the workshop, possibly including some preparations on beforehand, is awarded with 1 ECTS credit.

Registration: The number of slots are limited and priority is given to SLU PhD students. To register on first come first served basis, send an e-mail to Lea.Wittorf@slu.se before May 16.

Organism Biology seminar

How to transfer your academic skill sets to industry - transferable and soft skills perspective

June 10th 13:00-17:00 - Biocenter, lecture room A241

How to get your dream job? As you prepare to find your passion among the ecosystem of alternative career paths, you need to be aware that job market needs is not enough to find your dream job. Once you understand what your chosen job niche is, you need to look inwards to acknowledge your soft and hard skills and market yourself well. 
As scientists prepare to step out of the comfort zone and leave academia, we struggle to put our skills into a language that would make us appealing to the job market. The Organism Biology Research School offer an afternoon seminar and pizza-pub with the aim of helping you into the career market beyond academia.
 In this seminar, Tina Persson, a certified career coach, will guide you through the process of rebranding yourself and translating your academic merits into an appealing language for industry. You will leave the seminar with stronger self-awareness and confidence on your abilities, feeling empowered to demonstrate your value and what you can offer to employers from different sectors. The seminar will be immediately followed by a pizza-pub, setting the right atmosphere for informal follow-up discussions with Tina and your fellow colleagues.

 This seminar is offered in conjunction to the 10th Annual Organism Biology Workshop: Apply for your future, June 18-19, but is open to everyone.

Please submit your registration by mail to Lea.Wittorf@slu.se before May 31, and state whether you will also attend the pizza-pub. The number of participants is limited to 30. Please note that the deadline for registration to the Annual Organism Biology Workshop is May 16!

Confocal Microscopy, 5 ECTS (PNS0138)

May 2 – 17, 2019

The aim of this course is to provide students with a solid theoretical background essential for designing confocal microscopy experiments, introduce them to the most common softwares used in the area and also to give students hands-on experience with confocal microscopes available at the BioCenter and SciLifeLab, UU. All lectures and seminars of the course will be open for the public, registration is required only for the practical part of the course and for obtaining the credits. For information about the course schedule and syllabus see attached pdf files. To register for the course, send an e-mail to Adrian Dauphinee (adrian.dauphinee@slu.se) no later than April 12th, 2019. Number of participants limited to 15.

Understanding & Coding the R Programming Language, 2 ECTS

April 1-5th 2019

PhD course and an opportunity to learn more about programming in R.
Apply by sending an e-mail to the course leader Matt Low (matthew.low@slu.se) – no later than Friday March 1st.

Visualize your Science, 4 ECTS (PNG0073)

Part time from March 26 to June 5

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake.
 
The course is software independent and will cover things like use of colors, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know
- How to create beautiful and credible scientific posters.
- How to use professional illustration software to illustrate your research.
- Where to find images, if you cannot draw them yourself.
- How to create images that are simple but yet informative.

The course runs on part time from March 26 to June 5. It represents a mix of online theory and drawing tutorials and face-to-face feedback sessions.

For more info about the course, see the syllabus and the schedule attached. You can also visit the course home page at https://visualizeyourscience.com/vys_spring. The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see the short résumé attached.

The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For binding registration on first serve basis (student number limited to 20), send an e-mail before March 20 to Mattias.Thelander@slu.se indicating your name, department and position. In principle, all costs for the course are covered by the research school Organism Biology. The one exception is if a registrant does not show up for the course without informing the organizer in due time.

• Schedule
• Syllabus

Friday March 15th, 2019

Welcome to the seminar where you will meet representatives from the Swedish research councils Formas and VR, the union (SULF), and several post docs. We have also invited two researchers that will discuss and give you their perspectives on writing applications and evaluating applications.

Global Sustainable Development Goals & Swedish Environmental Quality Objectives, 1 ECTS (PNG0079)

8th of February 2019

The purpose of this workshop is to increase our awareness for the Global Sustainable Development Goals (SDG) and the Swedish Environmental Quality Objectives (EQO), as well as how they relate to our research. Get a deeper understanding about possible conflicts and synergies when working with the SDG and EQO regarding environmental monitoring, research, and other commitments under international agreements.

Career Outside University for PhDs

One day seminar Thursday 29th of November 2018, Ultuna
More information is available here (pdf-format).

How to write and publish a scientific paper (4.5 HEC)

The students work on their own manuscripts throughout the course, integrating theory and practice. Constructive feedback and analysis of these texts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a manuscript ready for submission. The course will also include additional exercises and analysis of already published material.

The course will be run at BioCenter, Uppsala, with start on the 29th of October 2018 and continue until 25 February 2019. Scheduled activities are eight group sessions (2h) approximately every two-three weeks. Additional studies (not scheduled) consist of literature studies and written exercises.

The number of participants is limited to 10. Priority will be given to members of the Organism Biology and Focus on Soils and Waters research schools but is open also to other PhD students. Deadline for application is 15^th of October, 2018.

Register by sending a mail to Mårten Lind: marten.lind@slu.se

Visualize your Science, 4 ECTS (PNG0073)

Part time from October 10 to December 7
We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and t the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake.

The course is software independent and will cover things like use of colors, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know 

• How to create beautiful and credible scientific posters.
• How to use professional illustration software to illustrate your research.
• Where to find images, if you cannot draw them yourself.
• How to create images that are simple but yet informative.

The course runs on part time from October 10 to December 7. It represents a mix of online theory and drawing tutorials and face-to-face feedback sessions.

The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas and his contact info, see the short résumé attached.

All costs for this course is covered by the research school Organism biology. The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For registration on first serve basis (student number limited to 20), send an e-mail before September 12 to Mattias.Thelander@slu.se indicating your name, department and position.

• Schedule
• Syllabus

Advances in Enzyme Regulation (5 HEC)

November-December 2018
The course will focus on recent advances in chemical biology, with emphasis on enzyme regulation. You will learn about drug design and high-throughput screening, single-molecule imaging and cryo-electron microscopy, guided nanomolecular assemblies and enzyme engineering, N-terminomics and discovery of intrinsically disordered proteins. The program includes two modules: lectures on above topics delivered by world leading experts and training in writing research proposals.

Contact: Peter Bozhkov and Galia Zamaratskaia

Read more on the course web page

Sample preparation for high-throughput sequencing

3 HEC, 12-16 February, Ultuna

This intensive course aims to provide students with practical training as well as theoretical background for collection, handling and preparation of samples for highthroughput DNA and RNA sequencing of environmental communities. Participants will become well acquainted with all practical steps and familiar with their theoretical background and main pitfalls. The course also offers students opportunities to discuss their own sampling and sequencing methods and bioinformatics tools. The course consists of preparatory literature reading and a one-week meeting with short presentations of own work, lectures on theoretical background, and an intensive laboratory exercise (five half-days) where all steps in the sample preparation protocol will be trained, using soil fungal communities as an example.

Read more about the course Sample preparation for high-throughput sequencing here.

Understanding and coding the R programming language, 2 ECTS

In collaboration with the research school ecology. Will run in May.

Multivariate methods for ecologists, 4.5 ECTS

12 Feb – 2 March

The course aims to illustrate a number of factors which should be considered in multivariate analysis of ecological data. The course will concentrate more on the selection of relevant methodology (e.g. application of multivariate methods), than on the underlying mathematical aspects of the various statistical procedures. After completing the course, the student will be able to apply multivariate methods for analysing their own data, as well as to understand and assimilate more advanced literature. The course is given in collaboration with the research school Focus on soil and water.

Read more about Multivariate methods for ecologists here.

How to become a postdoc (1 day workshop)

One day workshop that will be arranged together with the research school Ecology and Focus on soil and water. Is planned to take place in March. It depends on when representatives from Formas and VR can participate.

Annual workshop: Focus on the academic career, 1 ECTS

The annual workshop will take place at Högbo bruk the 12th-13th of June and the theme for this year will be “Focus on the academic career”.

Plant Microbe Interactions, 6 ECTS

January 16 to March 16, 2018.
Plants and microbes interact in many different ways. In the postgraduate course “Plant-microbe interactions”, interactions between plants and microbes are discussed on general and detailed level for both pathogenic and symbiotic interactions. Infection mechanisms, establishment of symbiotic relations, plant defence and stress responses as well as many important problems within agriculture, horticulture and forestry are brought up.

The course is supported by the graduate school Organism Biology and organized in collaboration with Helsinki University and Norwegian University of Life Sciences. The lectures are given by the three universities and shown through videoconference equipment to the distant sites.

To apply, please send an email to the course leader Daniel Hofius (daniel.hofius@slu.se) latest January 12.

• Schedule for Plant Microbe Interactions
• Syllabus for Plant Microbe Interactions

Visualize Your Science, 4 ECTS, 17th April, 3rd May, 22nd May, 8th June

We all do excellent research that deserves to be presented in the best possible way. This course is open to you who wants to improve your skills in drawing figures, making posters and visually convey your research more effectively to both peers and t the general audience. The goal of the course is to teach you basic skills that will make you comfortable to do figures that are clear and crisp, posters that outshine your neighboring fellow posters and presentations that keep your audience awake. 
 
The course is software independent and will cover things like use of colors, text and typography, sins and working designs, mini art school, layout compositing, format/copyrights and where to find figures, software, basic infographics, tips and tricks and practical drawing sessions. You will also learn to master a drawing program of your own choice.

After the course, you will know 

• How to create beautiful and credible scientific posters.
• How to use professional illustration software to illustrate your research.
• Where to find images, if you cannot draw them yourself.
• How to create images that are simple but yet informative.

The course runs on part time from March 23 to June 8. It represents a mix of online theory and drawing tutorials and face-to-face feedback sessions.

The course is organized and taught by Andreas Dahlin at Visualize your Science AB on behalf of the SLU graduate school Organism Biology. To learn more about Andreas, see a short résumé at the end of this message.

All costs for this course is covered by the research school Organism biology. The course is primarily intended for PhD students within the SLU Graduate School Organism Biology but is open to all PhD students at SLU. Other SLU staff is welcomed if space allows. For registration on first serve basis (student number limited to 20), send an e-mail before March 20 to Mattias.Thelander@slu.se indicating your name, department and position.

• Course Syllabus
• Time and Place for face-to-face sessions 
• About the course organizer

Introduction to Bioinformatics using NGS data, 2 HEC

Example of activities 2017

Practical NMR course in structural analysis, 20-30 January 2017

Protein Structure Hands-On Workshop, 15-19 May 2017

Transposable elements: Genomes and their epigenetic regulation (1.5 credits)

Part time Sept-Oct, 2016

In this PhD course essential topics of transposable element biology with an emphasis on molecular genetics aspects in plants will be covered. The aim of this course is to deepen the knowledge about transposable elements and to develop the skills needed to explore the latest trends within the topic area through reading the assigned literature and discussion. The course will primarily cover the following aspects:

• History of transposable elements
• Classification and variation of repeat sequences
• Transposable elements in genome evolution
• Transposable elements as genetic/genomic tools
• Definition and identification tools (methodology in dry and wet)
• Regulation and control of transposable elements by the host: influence of RNA silencing and epigenetic pathways
• Transposable element effect on gene regulation & domestication
• Transposable element dynamic regulation during plant development

The course will consist of six lectures/discussion sessions preliminary scheduled for September 29 and October 6, 7, 12, 14 and 20 (dates are relatively flexible and can be subjected to minor changes to match attendee's preferences). For further information about the course, see the attached Syllabus.

Confocal Microscopy (5 credits)

Sep 20 – Oct 5, 2016

The aim of this course is to provide students with a solid theoretical background essential for designing confocal microscopy experiments, introduce them to the  most common softwares used in the area and also to give students hands-on experience with confocal microscopes available at the BioCenter and SciLifeLab, UU. Students will also meet experts from SciLifeLab in Stockholm and Chalmers to learn about other microscopy technologies available in Sweden.

How to write and publish a scientific paper (4.5 HEC)

18th of August 2016 – 26th of January 2017

Scientific writing is an acquired skill that can be learned. This course provides instructions on how to structure and format each section of a scientific manuscript according to the IMRAD format, based on the book ‘Writing Scientific Research Articles: Strategy and Steps’ by Margaret Cargill & Patrick O’Connor (2009). Focus is placed on basic writing skills, particularly on how to write clear and concise sentences, paragraphs and sections. We will also discuss how to best present data in figures, how to use references and how to apply reference software appropriately.

The course consists of a mixture of lectures, and students will work individually on their own manuscript. As such theory and practice are integrated throughout the course. Constructive feedback and analysis of the manuscript drafts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a manuscript ready for submission. The course will also include additional exercises and analysis of already published material.

The course will start on the 18th of August 2016 and continue until January 2017. Scheduled activities are eight group sessions (2h) approximately every two-three weeks (see attachment). Additional studies (not scheduled) consist of literature studies and written exercises.

The number of participants is limited to 10. The cours is a cooperation between the research schools Focus on Soils & Water and Organism Biology. Priority will be given to members of these research schools but is open also to other PhD students.

Course timetable

8th annual Organism Biology workshop: Science Communication

7-8 June 2016, Älvkarleö Herrgård

 We cordially invite PhD students, supervisors and other members of the  research school to the 8th annual Organism Biology workshop. This year’s  workshop will include mini-workshops on hands-on communication skills,  lectures on scientific integrity and the art of applying for grants with  a smile, and research presentations from senior scientists and PhD  students. As usual the workshop will include social networking  activities and time for informal discussions.

Program

Mini-workshops

• Presenting your science – tips and tricks for talks and posters Cajsa Lithell, RedCapDesign 
• How to pitch professionally - captivate your audience with convincing rhetorics Lina Horndahl, ProPitch 

Adressing science integrity

• How explain the difference between science and pseudoscience to non-scientists? Prof. Dan Larhammar, Uppsala University and VoF
• Scientific misconduct - sadly not only the Macchiarini scandal   Prof. Dan Larhammar, Uppsala University and VoF

Inspirational lectures 

• Low-methane and high-yield rice for the planet Chuanxin Sun, SLU 
• Getting the FUNding - why applying for grants is fun Anna Rosling, Uppsala University

Practical information

Target group: PhD students, supervisors and other members of the Organism Biology research school 
Venue: Älvkarleö Herrgård located about 60 minutes away from Uppsala by bus (www.alvkarleoherrgard.com/). 

Call for proposals for targeted reading courses

Targeted reading courses are intended for a subset of Organism Biology members to obtain in depth knowledge about specific subjects. By keeping a focused scope and simple format allow courses on topics of interest only to a small group of PhD students to be swiftly set up on request. A targeted reading course can be proposed by any member of the Organism Biology graduate school and a senior researcher with in-depth knowledge about the topic will function as the course leader. The graduate school Organism Biology will provide administrative and financial support.

Real Time Quantitative PCR (4.5 credits)

May 3 – May 31, 2016

Real-time quantitative PCR is a very popular method broadly used and missused in molecular biology. The aim of this course is not only to teach the very basics of the qPCR theory and practice, but also to introduce students to the MIQE guidelines essential for designing performing and interpreting quantitative experiments in a reliable way. Another aim of this course is to familiarize students with more advanced technologies alternative to qPCR which are gradually becoming more and more available. Students will get the opportunity to meet with experts in next generation sequencing and microarray assays.

All lectures and seminars of the course will be open for public,registration is required only for the practical part of the course and for obtaining the credits.

To communicate science

April 25-27 and May 25-26

The PhD course “To communicate science” provides you with tools to efficiently convey your research to the general public.Being able to communicate new knowledge and facilitate research application is of increasing importance to scientists - not to mention in obtaining research grants. 

During the course you will learn how to plan and perform effective communication, using different methods and different channels, depending on what audience you want to reach. You will also gain awareness on how to avoid difficulties and misinterpretations.

The PhD course “To communicate science” is arranged jointly by research schools “Food in focus”, "Organism Biology", "Focus on Soils and Water", "Ecology" and "Society, Landscape and Land use" and the division of communication at SLU.

The course is open for all PhD students at SLU and gives 2 credits. The course is given in English and the number of participants is limited to a maximum of 15. The course location is Uppsala.

How to become a post-doc - Workshop

Wednesday March, 9.00 -16.00

Welcome to a seminar where you meet representatives from the Swedish research councils Formas and VR, the union (SULF), and several post docs. We have also invited professor Hjalmar Laudon (SLU-Umeå) to present tips and valuable advice on how to write successful applications.

Come and learn about what is required to apply for funds or positions, why you should do a post doc, possibilities to keep your social benefits during your post doc time and what other things may be important to consider. Coffee and lunch is included. The workshop takes place in Tammsalen at Ekologicentrum, Ulls väg 16, Ultuna campus (bus stop Veterinärvägen).

Organizers: the SLU NJ-faculty research schools: Bioenergy, Ecology, Focus on Soils and Water, Food in Focus, Organism Biology, and Society, Landscape and Land use.

Programme 

Understanding & Coding the R Programming Language

April 11th - 15th 2016 (week 15)

A PhD course and an opportunity to learn more about programming in R.

Plant-microbe interactions, 6 HEC, (PNS0079)

January 21 to March 25

In the postgraduate course “Plant-microbe interactions”, interactions between plants and microbes are discussed on general and detailed level for both pathogenic and symbiotic interactions. Infection mechanisms, establishment of symbiotic relations, plant defence and stress responses as well as many important problems within agriculture, horticulture and forestry are brought up. The course is supported by the graduate school Organism Biology and organized in collaboration with Helsinki University and Norwegian University of Life Sciences.

The lectures are given by the three universities and shown through videoconference equipment to the distant sites. The postgraduate course is arranged as a part of the MSc course “Plant-microbe interactions” and contains 21 lectures, literature studies using recent review articles, discussion of study questions and a final written exam.

Career outside university for PhDs

October 22

Do you want to pursue a career outside of academia? Have you asked yourself what possibilities you, as a PhD, have in the labor market outside of the university? Do you want to improve your chances of finding your dream job! Then this is an excellent opportunity!

This workshop include discussions and exercises about different aspects of finding your career path including how to identify and value your competences and skills and how to write an excellent CV and job application. In the afternoon invited former PhD students employed at authorities and private companies will share their experience and points of views on pursuing a career outside of academia.

How to write and publish a scientific paper (4.5 HEC)

Scientific writing is an acquired skill that can be learned. This course provides instructions on how to structure and format each section of a scientific manuscript according to the IMRAD format, based on the book ‘Writing Scientific Research Articles: Strategy and Steps’ by Margaret Cargill & Patrick O’Connor. Focus is placed on basic writing skills, particularly on how to write clear and concise sentences, paragraphs and sections. We will also discuss how to best present data in figures, how to use references and how reference software can be useful.

The students work on their own manuscripts throughout the course, integrating theory and practice. Constructive feedback and analysis of these texts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a manuscript ready for submission.

The course will be run at BioCenter, Uppsala, with start on the 27th of October 2015 and continue until March 2016. Scheduled activities are group sessions (2h) approximately every two-three weeks. Additional studies (not scheduled) consist of literature studies and written exercises. The course book will be provided.

RNA-seq course, 2 HEC

Nov 23-25 + Dec 10

This course, organized at the Ultuna campus in Uppsala, provides a comprehensive theoretical and practical introduction to RNA sequencing.

The course starts with three intense days (Nov 23-25) of lectures and computer exercises provided by Johan Reimergård and colleagues at WABI and SciLifeLab. Lectures will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis.

Individual assignments will then help participants to process acquired knowledge and integrate it in their own research projects. These assignments are carried out at the home department with guidance from Johan Fogelqvist as needed, and are reported and discussed in a final get-together on Dec 10 to conclude the course.

The course is primarily intended for members of the Organism Biology research school but is open also to other PhD students and researchers. There is no tuition fee. The maximum number of participants is set to 20.

To register for this course, basic knowledge in linux is an absolute requirement. If you lack such previous knowledge, we recommend that you keep your eyes open for the “Linux Introductory Course” organized by Marcus Holm at UPPMAX. This four days crash course is planned for October but has not yet been officially advertised.

Evolution – effects on genes, individuals and populations, 4 HEC

30 Nov - 2 Dec, 2015 20 Jan - 22 Jan, 2016

In this postgraduate student course we will highlight the nature of population genetic and evolutionary processes and their impact on genes, individuals and populations. Aspects that will be covered include population genetic processes (i.e. selection, genetic drift and gene flow, mutation), molecular evolution, epigenetic mechanisms and speciation. Basic concepts and underlying mechanisms will be covered alongside with an introduction to the methods and tools that are used in these research areas. Exercises, discussions and individual assignments will help participants to integrate acquired knowledge in their own research projects. The course is built up around two three-day blocks of lectures, exercises and discussions separated in time to allow work with individual assignments at the home department.

Teachers will represent a mix of in-house experts and renowned invited guests. The course is organized jointly by Anna Lundhagen (Ecology), Magnus Karlsson (Forest Mycology and Plant Pathology), Sofia Berlin Kolm (Plant Biology) and Mattias Thelander (Plant Biology) on behalf of the research schools Organism Biology and Ecology – basics and applications.

Multivariate methods for molecular community analyses

October 12-16

This course will provide a comprehensive introduction to multivariate analysis methods applied on sequence data from microbial community studies. The course is one week full time consisting of theoretical lectures and computer exercises combined with individual literature studies of selected scientific papers. Aspects that will be covered include data properties and data handling, ordination, classification, hypothesis testing incl. PERMANOVA and generalized linear models as well as phylogenetic based methods.

We will mainly use the commercial software CANOCO v.5. SLU affiliated students can have the program installed. Students used to R may use R for the exercises. We will do all exercises at a computer lab. You may use your own laptop.

The course is organized by Ulf Grandin (Aquatic Sciences and Assessment) on behalf of the research school Organism Biology and teachers included are Claudia von Brömssen (Economics, Unit of Applied Statistics and Mathematics), Björn Lindahl (Soil and Environment) and Sara Hallin (Microbiology).

The course is primarily intended for members of the Organism Biology research school but is open also to other PhD students. There is no tuition fee.

Scientific creativity and creative science

2-3 June 2015, Högbo Brukshotell

We cordially invite PhD students, supervisors and other members of the research school to the 7th annual Organism Biology workshop. This year’s workshop will explore the role of creativity in science and give ideas on how to make the most of your own creativity!

Program highlights

Mini-workshops

How findings from modern psychology can be used to boost creativity
Niklas Laninge, Psykologifabriken

The influence of exercise on bodily and mental functions
Carl Johan Sundberg and Jessica Norrbom, Physiology & Pharmacology, KI

Inspirational lectures

Ancient DNA and human evolutionary inference
Mattias Jakobsson, Ecology and Genetics, UU

What can fungal DNA learn us about the functioning of forest ecosystems?
Björn Lindahl, Soil and Environment, SLU

Forensic entomology - an inordinate fondness for insects and death
Anders Lindström, National Veterinary Institute (SVA)

Other activities

• Creative discussion about future directions of the research school
• Social networking activities, time for informal discussions

Root-Soil-Microbe Interactions, 3.5 HEC

4-8 May

This course focuses on beneficial root-soil-microbe interactions in the rhizosphere context, and covers both agricultural and forest ecosystems. The aim is to give students a comprehensive overview of beneficial interactions taking place in the root-soil-microbe interface, including mycorrhiza, bacteria, archaea and root nodule symbioses. The course provides information on state-of-the-art applications and research subjects within the field.

The course consists of one intense week of full-time studies (4-8 May) preceded by individual literature studies of selected scientific papers. The scheduled course week includes lectures by invited national and international teachers, literature discussions and PhD student poster presentations. The lectures will be open for all interested students/researchers.  

Digital Images and Scientific Illustrations, 2 HEC

March 11 - 12 and April 28

Illustrations are important in all scientific publications. In this course you will get a mainly practical introduction to the handling of computer graphics and digital images. Focus is on photographs and self-made illustrations, but enhancement of graphical output from statistical software will also be covered. After the course you should be able to edit digital images and create figures and illustrations for publications. Software will first be demonstrated in a mixed lecture-workshop format (March 11 and 12). You will need to bring your own computer with the appropriate software installed (Adobe Photoshop and Adobe Illustrator version CS2 or later). You will then work on personal projects for an extended period at your home department, preferably figures for a publication or poster. Finally, projects are presented and discussed in a final get-together (April 28).

Plant-microbe interactions, 6 HEC, (PNS0079)

January 20 to March 25

 In the postgraduate course “Plant-microbe interactions”, interactions between plants and microbes are discussed on general and detailed level for both pathogenic and symbiotic interactions. Infection mechanisms, establishment of symbiotic relations, plant defence and stress responses as well as many important problems within agriculture, horticulture and forestry are brought up. The course is supported by the graduate school Organism Biology and organized in collaboration with Helsinki University and Norwegian University of Life Sciences.

The lectures are given by the three universities and shown through videoconference equipment to the distant sites. The postgraduate course is arranged as a part of the MSc course “Plant-microbe interactions” and contains 21 lectures, literature studies using recent review articles, discussion of study questions and a final written exam.

How to write and publish a scientific paper (4.5 HEC)

Scientific writing is an acquired skill that can be learned. This course provides instructions on how to structure and format each section of a scientific manuscript according to the IMRAD format, based on the book ‘Writing Scientific Research Articles: Strategy and Steps’ by Margaret Cargill & Patrick O’Connor (2009). Focus is placed on basic writing skills, particularly on how to write clear and concise sentences, paragraphs and sections. We will also discuss how to best present data in figures, how to use references and how reference software can be useful. The students work on their own manuscripts throughout the course, integrating theory and practice. Constructive feedback and analysis of these texts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a manuscript ready for submission.

The course will be run at BioCenter, Uppsala, with start on the 20th of November 2014 and continue until March 2015. Scheduled activities are group sessions (2h) approximately every two weeks. Additional studies (not scheduled) consist of literature studies and written exercises.

Introduction to Bioinformatics using NGS data (2 HEC)

8-12 December

The course will provide an introduction to a wide range of analytical techniques for massively parallel sequencing, including basic linux commands. Lectures on the theory of analysis algorithms will be paired with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs.
Topics covered will include;

• NGS read-to-reference alignment (genomic and RNA-Seq) 
• Variant calling in populations 
• De novo assembly of genomic and RNA-sequence data 
• RNA-Seq expression analysis

Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data. 
A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable and in order to get the maximum benefit from the course we would like you to; 

• have relevant previous experience in sequencing or analysis 
• have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing 
• Be able to bring your own laptop for the practical computational exercises

The course is arranged in collaboration with SciLifeLab.

Real Time Quantitative PCR (7 HEC)

1-29 October

Real-time quantitative PCR is a very popular method broadly used and missused in molecular biology. The aim of this course is not only to teach the very basics of the qPCR theory and practice, but also to introduce students to the MIQE guidelines essential for designing performing and interpreting quantitative experiments in a reliable way.

Another aim of this course is to familiarize students with more adavanced techonologies alternative to qPCR which are gradually becoming more and more available. Students will have an opportunity to meet with experts from SciLifeLab and Functional Genomics Unit of Helsinki University and also learn how qPCR is applied in forensic science.

Confocal microscopy (7 HEC)

3 November - 10 December, 2014

Thanks to the rapid development of technology the fancy confocal microscopy is now available for every day use, this opens completely new horizons for both great discoveries and missing controls. The aim of this course is to provide students with a solid theoretical background essential for designing their experiments, introduce them to the most common softwares and also to give students an opportunity to have a hands-on experience with confocal microscopes available at the BioCenter and SciLifeLab, UU. Students will also meet experts from SciLifeLab, Stockholm and Chalmers to learn about other microscopy technologies available in Sweden.

Annual organism biology workshop

4-5 June

This year we will have a joint event together with the Doctoral school in Environmental, Food and Biological Sciences at University of Helsinki.

As usual, the program will be a mix of science and network promoting activities. Invited lecturers will introduce different aspects of the workshop theme – ‘Applied bioinformatics –useful tools to answer biological questions’.

The program is composed of four different sessions:

(1) Evolution and adaption

Prof. Mirko Rossi (Dept. of Food Hygiene and Environmental Health, University of Helsinki) will introduce the topic by presenting his work on the genomics of bacterial pathogens (Campylobacter and Helicobacter species) and Senior lecturer Jens Sundström (Dept. of Plant Biology, SLU) will talk about his research of the reproductive development of vascular plants, before the session  ends with some PhD student presentations. 

(2) Community structure and interactions

Prof. Sara Hallin (Dept. of Microbiology, SLU, Uppsala) will introduce the session by presenting her research in microbial ecology and 4 PhD students will be given the opportunity to present their research related to community structure and interaction in a broad sense.

(3) Function and regulation

In this session Prof. Gerhart Wagner will give the introductory presentation based on his research on small RNAs and their role in fundamental life processes. A couple of PhD students will have the opportunity to present their project work. 

(4) Poster session
Those PhD students not giving an oral presentation under the three above mentioned sessions will have the possibility of presenting their research project with a poster! 

Supervisors – you are also very welcome to participate in this workshop. This is a great opportunity to learn what the PhD students within the graduate school are working with and to network with colleagues from other departments and the University of Helsinki in a relaxed atmosphere.

The workshop will this year be held at Sunnersta Herrgård and at the SLU Campus. Accommodation and all meals are provided.

Innovation and Utilisation

-A workshop on how to make research ideas available to society through products and services. How can academic research be developed into various products and services available to society? What do you need to know? Where can you get help and support? 

Learn more about the support available and meet innovators and entrepreneurs from SLU, during a 2-day inspiring workshop that will give insights into the process of innovation and commercialisation of research ideas! 

The workshop is organized by the Research Schools Ecology – basics and applications, Bioenergy, Focus on soils and Water and Organism Biology together with SLU Holding.

Understanding Programming in the R Language

- tools for flexibility in the analysis process (2 HEC)

A PhD course and an opportunity to learn more about programming in R!
Organised by the research schools Ecology - basics and applications and Organism Biology

When: May 5-­9 2014 
Where: Akademihotellet, Övre Slottsgatan 5, Uppsala 
Who: Matt Low (Department of Ecology, SLU) will organize and teach the course 
What: You will get 5 days of intensive R programming experience – with fika & lunch provided 
Credits: 2 ECTS

How to become a post doc - workshop February 28

Are you planning on doing a post doc? Do you know where you can apply for funding? Do you need more information? 

On Thursday the 13th of February you are welcome to participate in a seminar where you meet representatives from the Swdish research councils Formas and VR, the union (SULF) and current and former post docs. Come and learn about what is required to apply for funds or positions, why you should do a post doc, possibilities to keep your social benefits during your post doc time and what other things may be important to consider. Coffee and lunch is included. The workshop takes place in Tammsalen at Ekologicentrum, Ulls väg 16, Ultuna campus.

Organizers: the SLU NJ-faculty research schools: Bioenergy, Ecology, Focus on Soils and Water, Food in Focus, Organism Biology, and Society, Landscape and Land use.

Workshop: Postdoc Information
Thursday February 13 2014, 9:00-15:00 
Tammsalen, Ekologicentrum, Ulls väg 16, SLU Ultuna

Programme

Take the opportunity to get a broader view of the frontiers of plant science and to meet researchers involved in this research!

PhD students within the Organism Biology and Ecology research schools now have the possibility of attending the Linnean Center for Plant Biology seminar series Plant Science Frontiers and earn HECs! The aim is to give students an orientation of the frontiers of plant science, in a very broad sense, and provide a possibility for students to meet international researchers in the field of plant science.

To earn 1 HEC, the student chooses 3 seminars from the Linnean Plant Science Centre seminar series “Plant Science Frontiers” to attend. Before each seminar there will be article(s) supplied which the student is expected to read before the seminar. The article(s) are discussed before the seminar together with the course leader and other students. After the seminar there will be a round table discussion with the invited speaker.

Digital Images and Scientific Illustrations, 2 HEC

Illustrations are important in all scientific publications. In this course you will get a mainly practical introduction to the handling of computer graphics and digital images. Focus is on photographs and self-made illustrations, but enhancement of graphical output from statistical software will also be covered. After the course you should be able to edit digital images and create figures and illustrations for publications. Software will first be demonstrated in a mixed lecture-workshop format (December 4 and 6).

You will need to bring your own computer with the appropriate software installed (Adobe Photoshop and Adobe Illustrator version CS2 or later). You will then work on personal projects for an extended period at your home department, preferably figures for a publication or poster. Finally, projects are presented and discussed in a final get-together (January 14).

Seminar series: Plant Science Frontiers (1 HEC) 

November 2013 – May 2013

Take the opportunity to get a broader view of the frontiers of plant science and to meet researchers involved in this research!

PhD students within the Organism Biology and Ecology research schools now have the possibility of attending the Linnean Center for Plant Biology seminar series Plant Science Frontiers and earn HECs! The aim is to give students an orientation of the frontiers of plant science, in a very broad sense, and provide a possibility for students to meet international researchers in the field of plant science.

To earn 1 HEC, the student chooses 3 seminars from the Linnean Plant Science Centre seminar series “Plant Science Frontiers” to attend. Before each seminar there will be article(s) supplied which the student is expected to read before the seminar. The article(s) are discussed before the seminar together with the course leader and other students. After the seminar there will be a round table discussion with the invited speaker.

Light and confocal microscopy (3 HEC)

Introduction to basic optical theory as well as the practical application of the theory for both conventional light microscopy and fluorescence microscopy; general histological specimen preparation techniques; specific localisation techniques such as immunohistochemistry. Photomicrography with analogue and digital cameras; Digital image processing. The course will be predominantly practical with most time spent on work with own samples. Lectures introducing the necessary theory on each aspect will precede the practicals. After the course the students should have the theoretical and practical knowledge needed to perform microscopical analysis of biological specimens with conventional light, fluorescence, and confocal microscopy. They should also be able to use digital image processing and analysis on the images acquired in the microscopes.

The course consists of three days of lectures with presentations of the theory behind different microscope techniques. These will take place 8-12 am on November 6-8. After that, there will be 3,5 weeks with individual practices on the microscopes using your own samples. The course ends with a seminar with presentations of your individual work on the course.

How to write and publish a scientific paper (4.5 HEC)

Scientific writing is an acquired skill that can be learned. This course provides instructions on how to structure and format each section of a scientific manuscript according to the IMRAD format, based on the book ‘Writing Scientific Research Articles: Strategy and Steps’ by Margaret Cargill & Patrick O’Connor (2009). Focus is placed on basic writing skills, particularly on how to write clear and concise sentences, paragraphs and sections. We will also discuss how to best present data in figures, how to use references and how reference software can be useful.

The students work on their own manuscripts throughout the course, integrating theory and practice. Constructive feedback and analysis of these texts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a manuscript ready for submission.

The course will be run at BioCenter, Uppsala, with start on the 8th of November 2013 and continue until March 2014. Scheduled activities are group sessions (2h) approximately every two weeks. Additional studies (not scheduled) consist of literature studies and written exercises.

Analysis of high-throughput sequencing data from microbial communities (3 ECTS)

27 Nov – 1 Dec

The course focuses on data analysis from high-throughput sequencing of fungal- and prokaryote communities. It encompasses one week of literature studies followed by an intense one-week workshop with lectures, demonstrations, student presentations and practices.

The course covers: 
- clustering and handling of sequence data 
- introduction to bioinformatics pipelines 
- diversity estimation 
- introduction to multivariate statistical analysis 
- taxonomic identification

The course is arranged together with the network NEFOM (http://www.nefom.dk/) and teachers include: Antonio Gonzalez (from the QIIME team), Henrik Nilsson (University of Gothenburg), Urmas Koljalg (University of Tartu), Jan Stenlid, Björn Lindahl and Sara Hallin (SLU) and others.

Research communication with the media - training and skills acquisition (2 HEC)

The course aim to equip you with skills and tools for effective communication of scientific results with the media. These skills will be provided through individual assignments, group exercises, discussions, feedback and guidance with professional journalists and communicators. You will prepare a mock press release and a popular scientific article about you research projects as well as drafting content for a personal homepage. Your texts will be discussed and you will get feedback. During the course you will also practice conducting and managing an interview about your PhD-projects on camera.

The course target group is PhD-students within research schools belonging to the NL-faculty. First priority will be given to registered students at the end of their PhD-studies (year 3 and 4).

Course dates: October 1-3, 2013 
Location: BioCenter, Uppsala 
Organizing Research Schools: Food in Focus, Organism Biology and Focus on Soils and Water

Metabolomics (3 HEC)

16-20 September

Metabolomics is the systematic study of the unique chemical fingerprints that specific cellular processes leave behind. It is widely applied in several areas of biological research including agronomy, nutrition, and medicine. Recent progress in high-throughput analytical technologies allows the simultaneous analysis of a large number of metabolites in different biofluids and tissues using advanced analytical approaches i.e. NMR and mass spectrometry methods. These analyses can potentially reveal a complex metabolic fingerprint characteristic of a given physiological status e.g. health and disease, dietary exposure, or a characteristic quality.

The course aims at hand-on experiment approach of metabolomics and provides the students with basic understanding of advantages and disadvantages of metabolomics, analytical strategies, statistical analysis and interpretation of metabolic alteration. The course starts with introductory lectures about the principle of NMR and mass spectrometry, multivariate statistics, and application of NMR and mass spectrometry in metabolomics analysis. Subsequently, students are assigned into metabolomics projects at the SLU metabolomics platform in different groups and will receive direct supervision for performing the experiment.  During the supervision meeting the student will discuss protocols and strategies for their respective metabolomics study. The course will be one intensive week based on review and research articles and internet resources including open-access databases and software.

By the end of the course, the students should be able to plan for investigating scientific problems using metabolomics in their relevant research field.

Course leaders: Ali Moazzami, Peter Agback and Corine Sandström

Annual organism biology workshop

28-30 May 
This year we will go to University of Helsinki to have an exchange with Prof. Fred Asiegbu and Prof. Jari Valkonen and their research groups as well as with the research school ‘Viikki Doctoral Programme in Molecular Biosciences’. As usual, the program will be a mix of science and network promoting activities. PhD students will get a chance to present their findings and ideas and the future of the research school will be discussed. The detailed program will be available in the near future.

Supervisors – you are also very welcome to participate in this workshop. This is a great opportunity to learn what the PhD students within the graduate school are working with and to network with colleagues from other departments in a relaxed atmosphere.

Phylogenetic analysis, 6 HEC (3 + 3 HEC)

Phylogenetic analysis is an important tool in modern biology. It is widely applied in several different areas of research including comparative genomics and epidemiology. A basic understanding of phylogenetics is also necessary to be able to interpret phylogenetic trees and asses their quality when analysing already published data. The aim of the course is to provide students with a basic understanding of phylogenetic analysis as well as an ability to perform phylogenetic analyses on molecular sequences.

The course is divided into two parts. The first 3 HEC part, 2-3 May and 13-15 May, consists of lectures and computer exercises describing methodology and invited speakers highlighting applications. The first part is concluded by literature studies and a written examination in August. During the second optional 3 HEC part, students will work on individual projects with their own data sets with supervision and weekly follow-ups. Projects are presented and discussed in a concluding get-together in the beginning of the autumn.

Course book: The Phylogenetic Handbook – A practical approach to phylogenetic analysis and hypothesis testing, eds. Lemey, Salemi and Vandamme. 2nd ed., 2009, Cambridge University Press.

Networking seminars

The networking seminars this semester will focus on how a future outside of academia can look like! Invited former PhD students now working in industries and governmental organizations will share their experinces with us. Take the opportunity to think about your future and build on your professional network!

We will meet either at lunch or later in the afternoon to listen to a presentation and then finish with discussions over food and drinks.

11 April - Anders Nilsson, GE Healthcare 
We will meet in BioC A-372 at 16.30
Anders was earlier a PhD student at Uppsala University 

2 May Matti Leino, Nordiska museet
We will meet in BioC A-402 at 16.30
Matti was earlier a PhD student at the Dept. of Plant Biology and Forest Genetics here at SLU

15 May - Jonas Toljander, National Food Agency (Livsmedelsverket) 
We will meet in BioC A-372 for a lunch seminar 12-13.30. Jonas was earlier a PhD student at the Dept. of Forest Mycology and Plant Pathology, SLU

5 June- Cajsa Lithell, RedCap Design
We will meet for a lunch seminar 12-13.30.
Cajsa was earlier a PhD student at the Dept. of Forest Mycology and Plant Pathology, SLU

How to become a post doc - workshop March 5

Are you planning on doing a post doc? Do you need more information? On Tuesday March 5 you are welcome to participate in a half-day workshop where you meet representatives from FORMAS, SULF and four post docs. Come and learn about what is required to apply for funds or positions, why you should do a post doc and what to think about. 

The workshop is a joint arrangement by the SLU graduate schools Bioenergy, Ecology and Organism Biology, Focus on Soils and Water and Food in Focus. Share the experience with former or ongoing post docs. Coffee and lunch included. Maximum 30 participants. 

Invasive and Emerging Plant Diseases (6 ECTS)

It has been known for years that new diseases can invade and become established in new areas and that diseases can emerge and cause serious disease problems reducing yield and product quality. However, we now experience an increasing threat of these emerging diseases due to global changes such as new ways of trading plant material and climate changes. Changes in production systems have also revealed new disease threats.

The course consists of different thematic sessions focusing on the main aspects of invasion biology, how invasion can be identified and what can be done to counteract establishment or emergence of new diseases in both agriculture and forestry. The course will provide a broad range of tools to the students - from modelling to population genetics. There is a red thread in the course helping students with linking theoretical concepts with real cases.

The course is a NOVA PhD course, please see more information on the NOVA web site 

Course date: 14-20 April 2013
Course venue: Älvkarleby, Sweden

Digital Images and Scientific Illustrations, 2 HEC 

Illustrations are important in all scientific publications. In this course you will get a mainly practical introduction to the handling of computer graphics and digital images. Focus is on photographs and self-made illustrations, but enhancement of graphical output from statistical software will also be covered.

After the course you should be able to edit digital images and create figures and illustrations for publications. Software will first be demonstrated in a mixed lecture-workshop format (November 27-28). You will need to bring your own computer with the appropriate software installed (Adobe Photoshop and Adobe Illustrator version CS2 or later). You will then work on personal projects for an extended period at your home department, preferably figures for a publication or poster. Finally, projects are presented and discussed in a final get-together (January 22).

Agrigenomics Dec 2012-Feb 2013

Do you want to learn and understand the principles of genomics with applications in animal and plant breeding? 

This course includes:

• Techniques for performing next generation sequencing and large scale genotyping
• Genome sequence analysis e.g. using genome sequence data for detecting selection, comparative genomics, genome evolution
• Methods for identifying genetic variation regulating complex traits, e. g. QTL mapping, eQTL mapping, association mapping, genome wide association mapping, genomic selection and marker assisted selection
• Practical applications of genome sequence data for breeding.

The course is based on attending lectures and participating in group discussions, computer labs and write a grant application that will be presented to the group. The lectures will be given by invited speakers with expertise in their respective fields. Sofia Berlin Kolm and Stefan Marklund will organize the afternoon sessions. The course is arranged within the SLU Research schools in Organism Biology (NL faculty) and Translational and Comparative Medicine (VH faculty)

Course start: 2012-12-14

How to write and publish a scientific paper (4.5 HEC)

Scientific writing is an acquired skill that can be learned. This course provides instructions on how to structure and format each section of a scientific manuscript according to the IMRAD format, based on the book ‘Writing Scientific Research Articles: Strategy and Steps’ by Margaret Cargill & Patrick O’Connor (2009). Focus is placed on basic writing skills, particularly on how to write clear and concise sentences, paragraphs and sections. We will also discuss how to best present data in figures, how to use references and how reference software can be useful.

The students work on their own manuscripts throughout the course, integrating theory and practice. Constructive feedback and analysis of these texts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a manuscript ready for submission. 

The course will be run at BioCenter, Uppsala, with start on the 25th of October 2012 and continue until March 2013. Scheduled activities are group sessions (2h) approximately every two weeks. Additional studies (not scheduled) consist of literature studies and written exercises.

Annual Organism Biology workshop 13-14 June 2012

This year we will go to Marholmen located on the east coast near Norrtälje. As usual, the program represents a mix of science and network promoting activities. Three broad and hot research areas will be highlighted, PhD students will get a chance to present findings and ideas and the future of the research school will be discussed. 

The program is composed of three different sessions: 
(1) Interactions
Professor Christer Björkman (Ecology, SLU) and Professor Peter Witzgall (Chemical Ecology Group, SLU, Alnarp) will introduce the topic and give examples from their research before the session is ended with short PhD student presentations. 
(2) Evolution and adaption
Sophie Karrenberg (EBC, Uppsala University) and Niclas Gyllenstrand (Plant Biology & Forest Genetics, SLU) will together with a few PhD students provide a broad picture of evolution and adaption.
(3) Organisms and their environment
Professor Jonathan Yuen (Forest Mycology & Plant Pathology, SLU) and Anke Herrman (Chemistry, SLU) will introduce the broad session theme from two different angles followed by PhD student presentations. 

Future of the research school, group discussions 

The four year funding period for faculty-funded research schools is coming to an end. What have we learned and what should be changed for the coming four years? 

Supervisors – you are also very welcome to participate in this workshop. This is a great opportunity to learn what the PhD students within the graduate school are working with and to network with colleagues from other departments in a relaxed atmosphere. 

How to become a post doc - workshop March 9

Are you planning on doing a post doc? Do you need more information? On Friday March 9 you are welcome to participate in a half-day workshop where you meet representatives from FORMAS, SULF and four post docs. Come and learn about what is required to apply for funds or positions, why you should do a post doc and what to think about. 

The workshop is a joint arrangement by the SLU graduate schools Bioenergy, Ecology and Organism Biology. Share the experience with former or ongoing post docs. Coffee and lunch included. Priority is given to third and fourth year PhD students. Maximum 30 participants. 

Electron microscopy and thermal analysis – applications in environmental and life sciences (3 HEC)

Physical chemical methods provide a combination of both average and detailed local characteristics of biological samples. Scanning electron microscopy gives insight into the morphology and the chemical composition and helps to visualize and identify functional parts and constituents in the objects of study. It is an ideal tool to follow the uptake of nutrients and microelements in plants and insects, determine the composition of minerals and follow the bio-digestion and biotransformation. Thermogravimetry is a versatile tool for determination of humidity in samples and of relative contents of biopolymers in plant (in the first hand, wood) tissues. All biological processes produce heat proportional to the rate at which given chemical or physical processes take place therein. These thermal flows can be measured by isothermal microcalorimetry – a non-destructive method – in environmental systems with very high precision. 

By taking this course you will learn and understand the principles and techniques applied in express-analysis and identification of biological processes and the chemical and morphological changes associated with them. The course will start on April 16th and will be running as full-time studies during week 16. It is composed of three blocks, comprising lectures, hands-on training and short individual projects, dealing with analysis and characterization of own samples. Projects are presented and discussed in a concluding get-together workshop on April 23. 

Teaching is provided by Vadim Kessler, Gulaim Seisenbaeva and Anke Herrmann from the Department of Chemistry at SLU. Prof. Jim Harris (Cranfield University, UK) will be a guest lecturer on this course. The number of participants is limited to 15 and registration is on first-serve basis.

Light and confocal microscopy (3 HEC)

Introduction to basic optical theory as well as practical application of the theory for both conventional light and fluorescence microscopy; general histological specimen preparation techniques; specific localisation techniques such as immunohistochemistry and in situ hybridization; photomicrography with analog and digital cameras; digital image processing. The course is predominantly practical allowing students to analyse their own samples, preceded by lectures.

Pizza seminars - an Organism Biology networkning activity

We continue our networking seminars after Christmas with invited speakers. We meet late in the afternoon to listen to a presentation and then discuss over dinner pizza. Build on your professional network by meeting possible future employers from industry and governmental agencies, and increase your knowledge about university related activities.

February 8: Pär Forslund, Director of studies for PhD education at the NL-faculty, SLU

April 17: Lars Erik Lindell, Grants Office, SLU

Presentations take place at Uppsala BioCenter from 16.30-17.30 and finish with discussions over food and drinks. Plant-microbe interactions (6 HEC, course code PNS0079)

Plants and microbes interact in many different ways. In the postgraduate course “Plant-microbe interactions”, interactions between plants and microbes are discussed on general and detailed level for both pathogenic and symbiotic interactions. Infection mechanisms, establishment of symbiotic relations, plant defence and stress responses as well as many important problems within agriculture, horticulture and forestry are brought up.

The course is given within the SLU Graduate School in Organism Biology in collaboration with Helsinki University and Norwegian University of Life Sciences. The lectures are given by the three universities and shown through videoconference equipment to the distant sites. The postgraduate course is arranged as a part of the MSc course “Plant-microbe interactions” and contains 21 lectures, literature studies using recent review articles, discussion of study questions and a final written exam.

The course runs from January 17 - March 23, 2012. 

Real time Quantitative PCR in theory and practice (3.5 HEC)

The Polymerase Chain Reaction (PCR) was invented in 1983 by Kary Mullis. Since then, the method has been much developed and now allows for the quantitative detection of minute amounts of specific nucleic acids in a sample in real time.

Real time quantitative PCR (RT-qPCR) is a reliable method used in basic biological research as well as in medical diagnostics, food security and forensic science. Despite its widespread use, first time users often find it demanding as both theoretical knowledge and hands-on experience often is needed to achieve enough accuracy in both design and execution of experiments. The aim of this course is to provide participants with the theoretical background essential for proper design of RT-qPCR experiments and to provide practical training in how to perform a RT-qPCR analysis including the interpretation and evaluation of obtained results.

The course consists of a mix of theoretical and practical elements and starts at 9 January and runs on part time until 25 January. In the theoretical part, necessary background information is provided in lecture format. In the practical part, participants will design and perform actual RT-qPCR experiments under supervision. Here, participants are encouraged to study expression of their own gene of interest in their preferred material. Results are then summarized in reports and discussed in workshop format. The course is finally concluded by a series of lectures by invited experts highlighting different RT-qPCR applications.

Research communication with the media: training and skills acquisition (1.5 HEC)

The course aim to equip you with skills and tools for effective communication of scientific results with the media. These skills will be provided through individual assignments, group exercises, discussions, feedback and guidance with professional journalists and communicators. You will prepare a mock press release and a popular scientific article about you research projects. You will also practice conducting and managing an interview about your PhD-projects on camera. 

Course dates: March 6-7, 2012 
Location: BioCenter, Uppsala
Organizing Research Schools: Food in Focus, Organism Biology, Ecology, NMRL and Focus on Soils and Water
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