Fall Student Orientation
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CSG Orientation Program for New Students, Postdocs, and Staff
Getting Started -- Aug 28 Thursday 2014 (1:30-3:30, M4332 SPH 2)[edit]
Introduction[edit]
- Welcome to CSG!
- Idea is to help new students and postdocs get oriented quickly within the group.
Cluster Architecture/Resources (Ryan, 30-60 min)[edit]
- Simple architecture setup
- Gateways versus project nodes
- Very brief intro to SLURM (used for submitting jobs)
- Slides located here: PDF
Disease Gene Mapping - Past, Present, and Future? (Jeroen, 1 hr)[edit]
- History of genetic epidemiology
- Where we are and how we got here
- Guide to critical papers
- Slides located here: PDF
First CSG Meeting in Semester[edit]
Efficient and Collegial Cluster Usage (Ryan, Sean, Terry)[edit]
- How to profile running programs for memory and disk/net IO
- How to submit jobs using SLURM, examples of submitting jobs
- How to check the status of your jobs and cluster usage
Sessions During Semester[edit]
If you would be interested in attending any of the following sessions, please fill out this poll.
Python (Ryan)[edit]
- 1-2 hour session
- We can go over the basics quickly, point everyone to resources they would need to learn through doing examples / code academy / etc.
- Also go over the "need to know" things about python, the most common packages that we use, etc.
- Go over a good development environment/setup for python (ipython, PyCharm, vim, debugging, etc.)
- Finally give some examples of doing "statistical genetics" work in python.
Perl (Terry)[edit]
R (Ryan, Xueling, others)[edit]
Unix Introduction[edit]
- Peggy White will give a Unix introduction to anyone who might be interested.
Projects and Studies within CSG[edit]
Boehnke Group Projects (Anne, Heather, postdocs)
- FinnSeq project (Large-scale Sequencing of Finnish Individuals)
- GO T2D/T2D-GENES consortia projects (Genetics Of Type 2 Diabetes and Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples)
- Tissue project
- BRIDGES project (Bipolar Research in Deep Genome and Epigenome Sequencing)
- METSIM study (Metabolic Syndrome in Men)
- D2D 2007 study (Dehko 2D)
- DIAGEN study (The Diabetes Genetics Study)
- DPS study (The Finnish Diabetes Prevention Study)
- DR'S EXTRA study (The Dose Responses to Exercise Training Study)
- FINRISK 2007 study (Coronary Risk Factors in Finland)
- FUSION study (Finland-United States Investigation Of NIDDM genetics)
- HUNT 2 study (Nord-Trøndelag Health Study)
- Tromsø 4 study
Abecasis Group Projects (Johanna, Mary Kate)
- SardiNIA Project (SardiNIA Study of Aging)
- AMD Project (Age Related Macular Degeneration)
- Psoriasis Projects
- Genes for Good Project (Facebook Project)
- iSeqTools (Software Improvements/GotCloud)
Past Course Notes / Useful Readings[edit]
Past Biostats class notes[edit]
- Statistical genetics concepts (Biostatistics 666: http://genome.sph.umich.edu/wiki/Biostatistics_666)
- Computational implementation of statistical methods (Biostatistics 615/815: http://genome.sph.umich.edu/wiki/Biostatistics_615/815)
- Special Topics in Analysis of High Throughput Sequence Data (http://genome.sph.umich.edu/wiki/Biostatistics_830)
