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Nigeria Takes Steps to Improve Bioinformatics Infrastructure

This Day, Nigeria’s daily newspaper, reported last week that Nigeria’s National Biotechnology Development Agency (NABDA) and the United Nations Education Scientific and Cultural Organization (UNESCO), sponsored a two-day bioinformatics training workshop in Abuja, Nigeria.

The workshop was supported by UNESCO’s Biotechnologies for Development in Africa project, an initiative to bring scientists in underdeveloped countries up to speed on the fundamentals of biotechnology.

Pauline Tallen, Nigeria’s minister of state for science and technology, told This Day that although Nigeria has not played a large role in genome sequencing, “with the introduction of training in bioinformatics, it is hoped that we would be able to get involved in post-genomics projects.”

Hubert Charles, UNESCO’s representative in Nigeria, said that the UN agency “will promote the application of best practices in the use of microbial germplasm, bioinformatics, and genetic engineering in the aquatic, environmental, and industrial biotechnologies, especially in small rural and island communities and countries in transition, to address issues of interdependence, novel agriculture, protection of the environment and poverty eradication.”

Food and water safety, as well as the HIV/AIDS pandemic and the emergence of other diseases, present particular challenges in underdeveloped countries that Charles said bioinformatics would play a role in addressing. In addition, he said, there may be economic benefits. “Bioinformatics and the life sciences are and will continue to replace physics and chemistry as the avenues of employment in labor, industrial, and socio-cultural markets of tomorrow.”

 

OmniViz Partners with Chemical Database Provider

Visualization software company OmniViz has entered a strategic alliance with chemical structure database firm BCI Ltd., the companies said last week.

Under the terms of the agreement, BCI will add its clustering technology for chemical structures to the data visualization and integration capabilities of OmniViz’s software.

While BCI’s algorithms effectively cluster large chemical datasets, “Thus far, we have lacked high-quality visualization tools,” said BCI director John Barnard in a statement. “Our collaboration with OmniViz will result in a uniquely powerful system that can overcome the significant informatics challenges currently facing industry, such as high-throughput screening data analysis and compound selection on very large datasets.”

According to OmniViz CTO Jeffrey Saffer, the current OmniViz software is able to cluster numeric, categorical, sequence, and free text information. “The added ability of clustering based on chemical structures furthers our lead as the only provider of an integrated visual analysis package for the life and chemical sciences sectors,” Saffer said.

 

Tripos Extends Debt Financing

Tripos said last week that it has nearly doubled its debt facilities with LaSalle Bank and its UK affiliate, ABN Amro Bank, to almost $13 million.

The financing now includes a revolving line of credit, a mortgage on US property, and a construction line of credit in the UK.

“These incremental facilities will be available to help fund working capital as well as capital expenditures related to our expansion efforts,” said Jim Rubin, senior vice president and CFO of Tripos.

 

DuPont Deposits Wheat Genome Data in GenBank

DuPont said last week that it has deposited all of its proprietary wheat genome data — more than 200,000 lines of ESTs — into GenBank.

The addition will more than double the amount of wheat genome data currently in GenBank, DuPont said.

The additional data is particularly valuable “because these specific ESTs were not previously represented,” said Olin Anderson, research leader with the US Department of Agriculture and coordinator of wheat and barley ESTs for the International Triticeae Mapping Initiative, in the UK.

“Making this data available, without restrictions, will bolster many ongoing research efforts and provide a foundation for the development of advanced varieties that benefit growers, breeders and consumers,” said Jim Miller, vice president, DuPont Crop Genetics Research & Development.

DuPont and its subsidiary, Pioneer Hi-Bred International, will continue their research on improved wheat varieties, the company said.

 

Sea Squirt Sequenced, Annotated, and Available Online

An international consortium of researchers led by the US DOE’s Joint Genome Institute published the draft sequence and initial analysis of the sea squirt, Ciona intestinalis, in Science last week.

By comparing Ciona’s genome with those of the human and other animals, the authors of the Science paper were able to glean new insights into the evolutionary origins of the human brain, spine, heart, eye, thyroid gland, and nervous and immune systems. About 80 percent of Ciona’s 16,000 protein-coding genes are also found in humans and other vertebrates, but the total number is only about half the number in vertebrates because Ciona has single copies of many genes that are present in multiple copies in vertebrates.

JGI enlisted the aid of the broad Ciona research community to augment its computational annotation of the genome, and convened an annotation jamboree last spring to review gene models, assign putative names and functional annotations, and explore the organism’s metabolic and regulatory networks and pathways.

Of Ciona’s estimated 16,000 protein-coding genes, 2,000 have been examined manually by the annotation team. This work is ongoing and available at www.jgi.doe.gov/ciona.

 

NAR Plans Web Software Issue

The journal Nucleic Acids Research is planning a special edition devoted to web-based bioinformatics software, to be published in July 2003, the journal said last week.

The special issue will be a companion to the journal’s annual database issue, which appears in January. Editors are seeking manuscripts describing programs that are accessible through the web “and perform interesting calculations or manipulations on DNA, RNA, and protein sequences and/or three-dimensional structures submitted to them,” according to a statement.

While these programs are valuable resources, “many are described only secondarily in other publications or have never been published and are found by word-of-mouth or chance,” according to the journal editors.

Like the NAR database issue, the entire web software issue will be freely available online.

For further information on submission requirements, contact R. J. Roberts ([email protected]). The final manuscript deadline is February 15, 2003.

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