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):

1. 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.

2. 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.