wiki:JessicaLog/2010-09-17

Version 1 (modified by trac, 14 years ago) (diff)

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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)

  • 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.

  1. 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.