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).
For registration on a first to serve basis (student number is limited to 12), send an e-mail before November 19 to joel.sohlberg@slu.se.
Syllabus
Schedule
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)
Prerequisites: Basic knowledge in molecular genetics is required. If more than people 20 have applied, students with phd studies relevant to agrigenomics will be prioritised.
Course start: 2012-12-14
Application deadline: 2012-12-03
Registration: Johanna.Boberg@slu.se
Syllabus
Team building, making a bird box. Photo: Johanna Boberg.
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.
The number of participants is limited to 10 and registration is on a first-serve basis.
Application deadline: 14 October 2012. -THE COURSE IS ALREADY FULL!
Information and application: Johanna Boberg
Course timetable
Syllabus
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.
Programme
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.
For registration send an e-mail before March 2 to Astrid Taylor with your name, affiliation and which year of studies you are in.
Tentative schedule
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. Deadline for applications is April 6, 2012. For further information and registration, contact the organizerVadim Kessler.
Syllabus
Schedule
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.
The course will be given part time February - March (starting February 29) at the Dept. of Mycology and Pathology, in collaboration with Uppsala University. Maximum 20 students. Registration deadline February 15, contact Cajsa Lithell.
Schedule
Syllabus
Summary course evaluation 2010
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
March 15: Cancelled
April 17: Lars Erik Lindell, Grants Office, SLU
May 8: To be announced
Presentations take place at Uppsala BioCenter from 16.30-17.30 and finish with discussions over food and drinks. For further information contact Petra or Mattias
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. To apply, or for further information, send an e-mail to the course leader Anders Kvarnheden latest January 13.
Syllabus
Preliminary schedule
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.
There is no tuition fee. The number of participants is limited to 20 and registration is on first-serve basis. For further information and registration, contact Alyona Minina. Deadline for applications is December 20, 2011.
Schedule
Syllabus
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.
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). For information and registration contact Petra Fransson.
Registration deadline: February 15, 2012
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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Syllabus