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NCBI to Retire LocusLink, Sun Seeks Bioinformatics Developers, BIGG, GeneBio, MSKCC Licenses GenomatixSuite, Inpharmatica, Accelrys, Natural Selection, Althea, Prolysis, Proteom


NCBI to Retire LocusLink March 1, 2005

As part of its transition from LocusLink to Entrez Gene, the National Center for Biotechnology Information said will stop updating LocusLink, and will “retire” the LocusLink web interface, on March 1, 2005.

“This decision was based on our having begun to provide complete extractions from Gene for ftp transfer,” NCBI said in an e-mail bulletin last week.

After March 1, LocusID-specific queries (of format[LocusID]) will be redirected to Entrez Gene, NCBI said.

NCBI has set up a web page to provide updates on the LocusLink/Gene transition at, and has also added a new report type category — “Comment on LocusLink/Entrez Gene” — to its feedback/corrections form (available at to accept comments on the transition.

Sun Seeks Bioinformatics Developers for Solaris 10 Porting Project

Sun Microsystems is recruiting developers of “significant” computational biology algorithms and databases for an initiative to port these resources to the upcoming Solaris 10 operating system on x86.

A free beta download of the operating system, which will be free and released under an open source license, is available at According to Sun, Solaris 10 will run on any x86 or Sparc CPU and will run Linux applications without modification.

Interested developers should e-mail Stefan Unger, Sun’s business development manager for computational biology ([email protected]), with their package name, a description of its functionality, the approximate number of active users or downloads per year, operating systems supported, CPUs supported, and a reference URL.

BIGG, GeneBio in Japan Distribution Pact

Geneva Bioinformatics said last week that it has signed a distribution agreement with the Bioinformatics Institute for Global Good (BiGG), a Tokyo-based research institute.

BiGG will establish “an extensive distribution campaign” for its Phenyx peptide mass fingerprinting software in Japan through its existing business relationships with Hitachi Software Engineering and bioinformatics software distributor Netwell, and in coordination with GeneBio’s Japanese branch.

MSKCC Licenses GenomatixSuite

Genomatix Software said last week that it has signed an agreement with Memorial Sloan-Kettering Cancer Center under which all of MSKCC’s 1,300 researchers will have unlimited access to the company’s GenomatixSuite bioinformatics platform.

Genomatix said it is working toward expanding the agreement to researchers at Rockefeller University and the Cornell Weill Medical College.

Shionogi Subscribes to Biopendium Online

Inpharmatica last week said that it has signed a non-exclusive agreement with Shionogi, a pharmaceutical manufacturer based in Japan, for a subscription to Biopendium Online.

Shionogi is the fifth Japanese subscriber to Biopendium and the third this year to use the online version.

PharmaDesign, Inpharmatica’s Japanese distributor, helped negotiate the agreement. MDL Information Systems markets Biopendium in the rest of the world.

Accelrys Grants Stock Options

Accelrys said last week that it has granted options to purchase its common stock to two employees who joined the company in October.

A total of 2,750 options were granted at an exercise price ranging from $5.93 to $6.10.

Natural Selection, Althea Partner on Gene Expression Biomarker Discovery

Althea Technologies, a gene expression analysis services provider, said last week that it is partnering with bioinformatics firm Natural Selection to co-develop a biomarker-discovery product.

NSI and Althea said they plan to create a product that will combine NSI’s computational methods for identifying gene signatures from expression data with Althea’s eXpress Profiling multiplexed PCR technology.

Prolysis to use Proteom’s In Silico Tools

Prolysis said last week that it has entered into an agreement with Proteom to use its in silico molecular design technology in its lead optimization program.

Prolysis will use Proteom’s ProtoScreen and ProtoBuild in silico screening and de novo design technology as part of development of antibiotics targeting bacterial cell division.

Financial terms of the agreement were not disclosed.


Filed under

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.