SysMO2 meeting, near Noordwijkerhout, Netherlands, June 7-9th 2010

As a member of the SysMO2 scientific advisory board, see http://www.sysmo.net, I attended the presentations given by the consortia funded by SysMO (Systems Biology of Model Organisms). The aim of SysMO is the development of system models. In most cases the consortia reported on new metabolomics datasets and the resulting models.

From the data management perspective this translates into two main deliverables supported by the SysMODB project http://www.sysmo-db.org. First, the data are deposited in spreadsheets based on shared templates designed in collaboration between SysMODB team and each project, and then either submitted to a central repository called SysMO-SEEK or linked to that database. Then, models are deposited in a model database called JWS, http://jjj.biochem.sun.ac.za/database/index.html. This website supports simulation.

Projects interact with SysMODB team via PALs (Project Area Liasons) who attend consortium wide meetings where they jointly discuss their data and processing requirements. Current work focuses on making SysMO-SEEK available as a toolbox for local installation and on extending JWS to cater for a wider variety of models.

Visit to Broad Institute

Today I had a short conversation with Anne Carpenter and Thouis Ray Jones at the Broad Institute in Cambridge (Boston). I have given her a short overview of our Swiss ‘landscape’ with SystemsX.ch, SyBIT and all the institutions working with us, and who is working on what in what context among the people they already interacted with. I also gave her a short functionality description also of openBIS and its relation to iBRAIN.

She said that the large-scale batch analysis of images was not such a high priority for them although they do have a prelimiary web service to provide cluster submission. Ray later said that they do run into scaling problems concerning file storage and large numbers of files sometimes, but it is not a very burning problem yet. They did not think about that yet.

They are interested in assuring that their tools can at least interface to our iBRAIN modules and would be willing to spend time to assure that this is the case, and reinforced their interest to host Pauli and Ela for a couple of days to discuss this.

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Perkin Elmer – Columbus Presentation

Today we have a presentation by PerkinElmer about their Columbus imange management system. Columbus builds on the Open Microscopy Environment (OME) set of tools, especially OMERO and the Bioformats library. It is capable of dealing with HTS data as well. Columbus provides image management by plate barcode, web interface showing thumbnails, including the acapella cell finding tool, etc. They claim to provide Columbus also as ‘Software as a Service’ solution, but cannot give numbers about remote data upload and remote data storage yet.

Basically the way this looked to me is that Columbus is a very nice well-done tool to look at individual plates and analyze them using some cell classification written in their own tool that depends on pipeline pilot.

They depend on OMERO to keep track of their data. Metadata on images is stored in xml files that are also tracked by OMERO. Since metadata is not kept in a db, they do not support filtering and searches on that, so this is a definite big weakness.

Concering large batch analysis of many plates the presenter gave me the impression that they have not considered that use case yet and do not intend to do so in the near future.

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