What I did
Setup and misc
- Setup molgenis.
- Went through molgenis tutorial.
- got the subclipse plugin and checked out the molgenis4phenotype, and eventually got it running (some possible defects with new molgenis + eclipse + macosx).
NGS LIMS
- Met with Jelke about protocols, obtained documents which were subsequently scanned in. (TODO: Create one pdf of all docs).
- Received an 'opdracht formulier' van Pieter v.d. Vlies.
- Created a folder on google docs for all info related to this project. https://docs.google.com/#folders/folder.0.0B3UX13npICWiN2M3OTg1ZjktMTBiYy00ZmUzLWIxZjgtOWQ3MjdhNzgyNjY0
- Researched alternative LIMS, created a wiki page with that info. LIM Systems. (TODO: add info about Genologics).
- Created a requirements doc. and populated with dna sequencing protocols
- Went over Pheno model with Erik.
- Uploaded docs from Jelke and mine's meeting
Literature / Personal Development (in my free time)
- Read pages 25 t/m 35 from "Intro to Bioinformatics" (Lesk).
- Completed lectures 4, 5, and 6 from Intro to Biology: http://ocw.mit.edu/courses/biology/7-014-introductory-biology-spring-2005/
- Read the first 2 chapters of Morris' thesis, "Dynamic Software Infrastructures for the life sciences".
- Installed IzPack? and started working on installer for molgenis.
- Made a basic installer (in Dutch and English), now working on nitty-gritty details.
TODO
- Create molgenis lims pilot
- Email Jelke with remaining questions (i.e. do all steps use "kits", what does a kit consist of, etc).
Finer detail (per e-mail exchange):
- Analysis of current and desired situation V1:
- I hope you have have copies from Jelkes notebook and order intake; that should help (could you put these as appendix?)
- For each of the steps in the flow chart: create an overview of what details are (should) be recorded (notes, parameters, files)
- Create some detailed user stories, optionally with some mock-up screen dumps, e.g.,
- Customers logs in and can see progress,
- Pieter logs in and can print cost statement,
- New customer inputs request for project
I have also included example of 'order form' from BGI http://dl.dropbox.com/u/1839500/formulier%20BGI.doc
Expected output: a document with the flow chart and then a paragraph on each step. For each step the input/output + description + example. So a bit more detail than you did now, merging your three documents => this will feed into step 2. In the end this will become the manual of our prototype.
- Create prototype V1:
- create a data model to capture each step, so formalize what you found in 1. Just hard-code each protocol | material | data element from you flowchart as entity, add descriptions and examples that you can copy from document 1 (molgenis_db.xml). In a later version we may want to use the 'Pheno' flexible data model. E.g.
<entity name="Sample"><description>Sample of DNA material provided by the customer</description> <field name="mgDNA" label="mg of DNA in solution" type="int" description="mg of DNA in solution. E.g. 32"/>...
- create example data for your model. Use a big excel file with each worksheet name == entity name and each column name == field name.
Let Erik or Joeri explain to you how you can easily import/export such excel into MOLGENIS.
- create a MOLGENIS demo where you have one screen for each step (molgenis_ui.xml).
Expected output: I expect here a system analogous to http://dl.dropbox.com/u/1839500/MOLGENIS_LIMS_example.ppt Most important for now is the data model; user interface enhancements come later. Note that each screen == entity == protocol | material | data/parameters from your flow chart.
