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Beta Release Cycle

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Sebastian Proost edited this page Jun 20, 2017 · 16 revisions

Upcoming releases

Beta 02 - Publicly available data for Chlamy, Arabidopsis, rice, tomato

To get feedback on co-expression networks, expression profiles, querying and comparative features from the EVOREPRO partners. To show tomato co-expression networks to AG-Fernie & CRAG (Barcelona) and get feedback on single-species features.

  • Complete 'single-species' features
  • Querying for tissue specific genes
  • Chlamy in PlaNet2
  • Arabidopsis in PlaNet2
  • Rice in PlaNet2
  • Tomato in PlaNet2
  • Analysis that reveals which gene families/Pfam domains are in common between two sets of genes (e.g. rice pollen vs. Ara pollen)
  • Analysis that reveals which gene families/Pfam domains are in common between > two sets of genes
  • Server config (MariaDB currently not running multi-threaded, apache mod_wsgi not running multi-processed)

From ITs/external sources, we need:

  • Access to phpmyadmin reinstated
  • Re-configure MariaDB on planet2 to run multi-processed/threaded
  • Test mod_wsgi parameters to run Planet2 multi-processed (avoid stalling under load)

Gold 01 - PlaNet2 release

NAR-web server would be ideal

  • Public Chlamy
  • Spruce
  • Arabidopsis
  • rice
  • maize
  • Sorghum data
  • Marchantia ?
  • Public Physco microarray data ? It's pretty good; on the other hand, it will be replaced with RNAseq.

From ITs/external sources, we need:

  • Additional disk space on planet2 server (Increase from 20 Gb to 50 Gb)
  • Alternatively: Run MariaDB on separate (virtual) machine with sufficient storage
  • Clear instructions what they require from the legal department to release a website 'in the wild', contact information for the person responsible for this. Detailed information what to add to the website (e.g. Impressum, ...)
  • Depending on usage the need for a load balancing might occur.

EVOREPRO Release Candidate 01: Consortium data and evolutionary features

  • Complete phylogenetic features (see Roadmap)
  • Process Public + EVOREPRO Amborella data (Regensburg)
  • Process Public + EVOREPRO Maize data (Regensburg)
  • Process EVOREPRO Arabidopsis data (Mark Johnson, Fred Berger)
  • Process Public + EVOREPRO Marchantia data ?

From ITs/external sources, we need:

  • All earlier requirements need to be fulfilled.

Older releases

Beta 01 (done)

For demo and workshop in Oeiras, 4 species (partial data for Maize) and functional annotation pulled from PLAZA.

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