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Lion, Bioinformatics.Org, SBML, Nirvana, Zambeel, BlueArc, Spinnaker Networks, Zzyzx, ProCom, Stonefly


Lion Puts Drug Discovery Tools on the Block

No longer looking toward a future in drug discovery, Lion Bioscience has put the discovery-related lab equipment from its San Diego headquarters up for sale.

DoveBid, a Foster City, Calif.-based auction house, is handling the two-part sale. A “negotiated liquidation” runs through Dec. 3, in which interested parties can inspect the equipment in person. The remaining pieces will be auctioned off during a webcast sale on Dec. 12 at 10 am PST.

Available equipment includes MicroMass and Finnigan mass spectrometers, a Varian NMR, high-throughput HPLC equipment, a Genevac system, robotics, and more.

Further information is available at:


Bioinformatics.Org Builds a Grid

Open source advocacy group Bioinformatics.Org has taken the first steps to build what it is calling the BiO Grid — a loosely networked cluster of bioinformatics tools that can be accessed by members of the organization for free.

The non-profit group is partnering with two companies in the initiative: Xinit Systems, a UK-based manufacturer of Linux systems; and GreenTea Technologies, a developer of distributed computing software.

Xinit Systems has provided an 8-node blade cluster and a 0.8 terabyte RAID array, which is located at its facilities in the UK and accessible via the Internet. GreenTea is providing licenses for its software for the Xinit cluster and will also provide licenses for other systems that are added to the grid in the future.

A mailing list has been set up for those interested in joining or using the BiO Grid at:


Next Level of SBML on the Horizon

SBML (the Systems Biology Markup Language) is going to have some new capabilities soon, according to Michael Hucka, a Caltech computer scientist and SBML developer.

SBML Level 1 was released in March 2001, and was intended to be “a simple format for representing models expressed as systems of biochemical reactions,” Hucka said.

While the language is capable of representing metabolic pathways, gene regulation, and signaling pathways, “it was always the intent to define additional levels of SBML after Level 1 in order to support more advanced constructs for those software tools that use them,” Hucka said.

The SBML developers are currently circulating a draft of the Level 2 specification, and several groups interested in SBML will meet on December 12 in Stockholm, immediately prior to the International Conference on Systems Biology, with hopes of finalizing the features of SBML Level 2. Hucka said a public specification may be issued early next year.

In addition to the work on SBML level 2, version 2 of SBML Level 1 is also in the works, with the goal of making it available on the website by December 10, Hucka said.

The Darpa BioSpice project and the I3C pathways working group are currently evaluating the Level 2 definition, Hucka said, and the SBML developers are also in discussions with the developers of CellML, another XML-based systems biology language, “to explore ways of making the two languages interoperable.”


Storage, Storage Everywhere

A walk around the exhibit hall at Bio-IT World earlier this month provided a good idea of what vendors think the life science IT market needs — storage, and lots of it. In addition to the usual suspects of IBM, EMC, and Network Appliance, a number of players new to the life science market were hawking their wares on the showroom floor:

Nirvana, a spinout from the San Diego Supercomputer Center, offers a solution called SRB (Storage Request Broker) that allows users to access data sources from remote locations via a single interface.

Zambeel provides an enterprise scale network-attached storage (NAS) system called Aztera that is optimized for large-scale storage requirements, according to the company.

BlueArc has been shipping its NAS system for just over a year, and claims Roche and Merck among its customers.

Spinnaker Networks is another NAS provider, and says that its ability to offer a single global file system sets it apart from its competitors.

Zzyzx (pronounced zee-zix) was founded in 1991, and offers SAN, NAS, and direct-attached storage solutions.

ProCom has been in the business since 1987 and offers the NetForce line of NAS products.

Stonefly specializes in storage area networks; specifically, what it calls IP SAN, which adds storage capability to a standard IP network.

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