Beta Release Cycle

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 - CoNekT release

NAR-web server would be ideal

• Public Chlamy
• Spruce
• Grape
• Arabidopsis
• Rice
• Tomato
• Maize
• Sorghum data
• Marchantia ? Not useful in public release
• 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. Not required

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 ?
• Process Physco 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.