What I did
DNA Sequencing / Background Reading
This week I spent learning about DNA sequencing, specifically next-gen sequencing. I started with Sanger's method (old-school) and working my way up to the most modern next-gen sequencing from Illumina, SOLiD, etc.
I also investigated Illumina's LIMS product and their GenomeStudio? in an attempt to find out what is offered and whether we would like their software or to build our own. On top of this, I investigated a data model that Joris had created, representing the GA process and the data that would need to be stored for such a backend.
Molgenis
I acquainted myself with the molgenis codebase and went through the tutorial. This brought me to the conclusion that an installer (and eventually wizards for setup) would be extremely handy.
TODO List
Objectives (in relation to NGS database/app):
- create a directory to collect 'all we know'
- create a word document that collects all requirements
- create a document with overview of the process analogues to Figure 1 in
http://bioinformatics.oxfordjournals.org/content/20/13/2075.full.pdf
- create for each protocol in the NGS process a summary description (input/output of materials/data/parameters)
- create a pilot MOLGENIS
=> Best use the version from SVN as described at http://www.molgenis.org/wiki/MolgenisSourceCode
- list and analyze some existing systems (Genalogic, system from collegues in Leiden and EMC if we can find them)
Actions for next week "get to a small pilot"
- Get some example 'opdrachtformulier' from Pieter
- Get detailed description of two or three protocol in detail, copying from Jelkjes book
- what parameters need to be captured
- what type of material go in and/or out
- are there additional data files (like configurations, images, tables)
- Install and learn MOLGENIS
- Learn the MOLGENIS 'pheno' model with Erik
- Test the entrance of the three protocols into this system (in animaldb there are also protocols and parameters)
