Agenda

Updates on iPToL projects

• Raxml-lite (John Cazes)
• CIPRES integration? (Sheldon)
• Trait Evolution (Naim Matasci)
• TNRS and Tree Reconciliation (Nicole Hopkins)
• Data Integration concerns (Val Tannen; Bill Piel)?

Notes

Raxml-lite (John Cazes)

· RAxML Light 1.0.2 has been released by Alexis. This version includes a memory saving feature that may reduce the memory footprint by a factor of 3. I'm currently testing this on Lonestar and Ranger with a 111K taxa case. However, it will probably take over a week to finish with restarts from checkpoint files.

· Alexis also released code for Parsimonator 1.0.0. This is a serial code that creates starting trees to be used for input into RAxML Light. It's based on the parsimony tree code in standard RAxML. It has been tested on both Lonestar and Ranger. The code creates a tree from a 116K taxa case provided by Alexis in ~55 hours on Ranger and ~24 hours on Lonestar.

· John is also in the process of developing a general batch script that may be used to initiate new RAxML Light runs or restart RAxML Light automatically from a checkpoint file.

CIPRES integration? (Sheldon)

· Waiting on information from Dan Stanzione on the outcome of CIPRES, the back-up plan is to use the My-Plant developers

· Sheldon spoke with Matt Vaugn on an update on the foundation API, it is coming soon

· Discussion on not losing momentum and progress if everything has to be evaluation, if there are projects that need to be in the fast lane, have a separate queue with high priority access that with work directly with our people.

ACTION ITEM: Naim and Sheldon will hold a separate meeting to discuss such governance.

Trait Evolution (Naim Matasci)

· Detailed TE notes https://pods.iplantcollaborative.org/wiki/display/iptol/TE110301

· match published trees with published data

· Collect datasets that can be used to teach evolutionary methods in classrooms

TNRS and Tree Reconciliation (Nicole Hopkins)

• Deployment of new algorithm, updated database and UI and services code for standalone should be complete by end of the week. This deployment will include the full name resolution (for trinomials until database is populated with USDA data). Deployment is meant to serve as initial user acceptance testing prior to incorporation of synonymy.
• UI code for synonymy and additional service to support resolution to accepted name work currently underway.
• Discussion with Bill Piel regarding inclusion of NCBI data to TNRS database. Initial thoughts were to add NCBI taxaIDs to the names found in the TNRS database. Brad and Bill to work on this effort. Goal would be to have database automatically update with NCBI data release.
• Discussion of extending TNRS schema to support resolution for internal nodes of a phylogenetic tree. This work will take place after addition of NCBI names in database. This will hopefully allow for resolution of data from the Big Tree. We will need to work out the details of how that would occur once we have the service in place.
• Discussion of web service requirements. API availability in discussion as well.
• TR - Working on obtaining open source license by end of the week

Data Integration concerns (Val Tannen; Bill Piel)?

· Sheldon is working with Val and Bill to make sure any concerns are addressed

Other items:

ACTION ITEM: Sheldon will facilitate a meeting with Gordon Burleigh and John Cazes later this week.