Oxford Summer School in Computational Biology 2011
Motivation and History
The Oxford Summer School in Computational Biology lasts for 6 weeks and focuses on doing research in contrast to attending lectures. Students will be working in groups of three on projects that are well planned and should have a high probability of leading to real progress on a real problem.
The Summer School grew out of an increasing number of successful summer studentships starting in 2003. In 2007 we had three summer students and one high school student. It became clear that collaboration between the students greatly enhanced the experience for everyone and that a detailed project description with references, clear goals and project milestones strongly increased the productivity of the students. This motivated us to expand our focus to several groups of students working together on more highly structured projects.
This year around twenty projects ideas were discussed beginning in late 2010, developed by a number of researchers both in the Bioinformatics group and in other Departments, particularly Plant Sciences. The projects were ranked according to how well-planned they were, their feasibility and potential level of interest for us and the students. The project descriptions went through a series of refinements in early 2011, such that we had a series of eight well-structured projects lined up by the beginning of the summer.
Goals
The main aims of the summer school are:
1) to give students a chance to experience working on highly relevant problems at the cutting edge of computational biology and bioinformatics
2) to make real progress on these problems, with a view towards publishing the results
3) to encourage applications for DPhils in computational biology and related subjects
Since 3 summer students, one graduate student and one postdoc work focused for 6+ weeks on each project, in total this corresponds to 6 months of well-planned work. The summer school allows us to undertake a series of exploratory projects, start new collaborations and test pilot projects for future DPhil projects and grant applications.
Projects
The topics eventually chosen in 2011 were quite diverse although a series of these had the common theme of evolution.
Lecturers
Each day, except where there are student/group presentations, starts with a 40-60 minute lecture at 8.30am. The lectures should give a a good impression of computational biology. The lectures are predominantly given by Oxford researchers, although we invite some from other universities and abroad.
| Steven Kelly (Plant Sciences) | Wim Hordijk (Lausanne, Switzerland) |
| Jotun Hein (Statistics) | Thomas Mailund (Aarhus University, Denmark) |
| Rune Lyngsø (Statistics) | Bela Novak (Biochemistry) |
| Adam Novak (Statistics) | Richard Mott (Wellcome Centre for Human Genetics) |
| Gil McVean (Wellcome Centre for Human Genetics) | Caleb Webber (Anatomy) |
| David Gavaghan (Computer Science) | Nick Jones (Physics) |
| Willie Taylor (NIMR, London) | Philip Maini (Mathematics) |
| Joe Pitt-Francis (Computer Science) | Philip Blunsom (Computer Science) |
| Carsten Wiuf (Copenhagen University, Denmark) | Elspeth Garman (Biochemistry) |
| Miltos Tsiantis (Plant Sciences) |
2012: students and current shortlist of Projects
We are aiming for 36 students working on 12 projects. Acceptance criteria for students will be highly selective and we are especially keen to encourage applications from students who are interested in potentially carrying out a DPhil in Oxford. Projects in the pipeline include:
| k-locus Generalization of Evans-Matsen Analysis | Inverse Folding II |
| Self-replicating Systems (three sub-projects) | Combining Multiple Levels of Annotations |
| Arabidopsis (annotation and recombination analysis) | Leaf Shape Evolution II |
| Machine Learning with Evolutionary Models | Annotation of Protein Interaction Networks |
| Evolving Dynamical Systems: The Cell Cycle | Approximate Genealogies |
We will also try one "virtual" project where three students aren't all in Oxford, but can guarantee to work full time and be in daily skype contact with instructors and each other.
Acknowledgements
At present, we obtain individual studentships for each student from EU, EPSRC, BBSRC and Nuffield. We are grateful to the Department of Plant Sciences at many levels including the use of computer rooms andt other facilities and to the Department of Statistics for their organizational help.
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