EBI to Lead €9M EU Systems Biology Software Project
The European Bioinformatics Institute said last week that it will coordinate a network of 20 experimental and computational labs across Europe in a project called ENFIN (Experimental Network for Functional Integration).
EBI said that the Commission of the European Union has awarded €9 million ($10.8 million) over five years to support the project, which will be led by the EBI's Ewan Birney.
Birney told BioInform at the Genome Informatics conference at Cold Spring Harbor Lab last week that the aim of the project is to develop new software tools that will allow bench biologists conducting high-throughput experiments to progress from "crude statistical associations" to more sophisticated kinetic models of biological processes.
Currently, he said, despite the availability of many public databases, most experimentalists end up analyzing their data in an Excel spreadsheet and matching the top-ranking genes to public resources. The project is envisioned as a means of analyzing that data in the context of biological knowledge.
"There are quite a few things to build," Birney said. The first year of the project will likely be focused on design decisions, with "internal" tool development through the next year and a half. "Usable tools" should begin coming online by the second year of the effort, he said.
Team Led by UCSC's Haussler to Reconstruct Whole Genome of Distant Mammalian Ancestor
It's technically possible to computationally reconstruct the genome of the ancestor of all placental mammals, according to David Haussler of the University of California, Santa Cruz, who is spearheading a collaborative effort to deliver the assembly of such a genome to the research community.
Haussler, a professor of biomolecular engineering at UCSC, said that an effort to "reconstruct the evolutionary history of each base in the human genome" from the time of the so-called Boreoeutherian ancestor, which lived around 75 million years ago, is "the grand challenge of human molecular evolution."
Speaking at the annual Genome Informatics conference at Cold Spring Harbor Laboratory, Haussler outlined several pilot studies that he and his collaborators have conducted as proof of principle for such a project. The group published a paper in the December issue of Genome Research describing the use of comparative genomics to computationally reconstruct the CFTR locus, which encompasses more than 1 million base pairs and includes 10 genes, including the gene involved in cystic fibrosis.
Since then, Haussler said, he and his collaborators including Webb Miller at Penn State University and researchers from the Broad Institute and the Baylor Human Genome Sequencing Center have used similar methods to reconstruct a region of human chromosome 13q and are moving on to whole-genome reconstruction.
Work so far "indicates feasibility," Haussler said, with an overall accuracy of around 91.5 percent a number he hopes to bring up to around 98 percent.
Haussler acknowledged that there is some skepticism about the accuracy of the reconstruction. But he said that he is confident in his team's method and validation process.
He and his colleagues have developed a software program to simulate the evolution of DNA over millions of years statistically accounting for substitutions, insertions, deletions, and other polymorphisms that arise over time and test this program on a hypothetical ancestral DNA sequence, artificially evolving the DNA to create simulated "modern" DNA sequences for multiple species.
Then they use their computational reconstruction procedure, which is based on multiple alignments of many species, to work backwards and recreate the hypothetical ancestral sequence. They can then compare the two versions of the hypothetical ancestral genome to determine the accuracy of the method.
After applying the reconstruction process to real genomic sequences, the team validates its predicted ancestral genome by simulating the evolution for organisms that are not included in the group from which the ancestral genome was derived. They can then compare the simulated evolved genome to the real one to gauge the accuracy of the predicted ancestral genome.
Haussler said that scaling the project up to the entire human genome is a "captivating" prospect that would provide valuable insights into human evolution, but would ideally use the full genome sequences of around 20 mammals far more than the National Human Genome Research Institute plans to sequence to completion.
"We have to keep sequencing genomes," he said.
Penn State's Miller told BioInform that the project is proceeding even with incomplete data, however. "We're not waiting," he said. "We're going as fast and furious as we can."
Miller said that the project is using the genomes of 11 organisms so far human, chimp, rat, mouse, dog, macaque, rabbit, cow, armadillo, elephant, and tenrec. Even though most of these have only been sequenced to very low coverage, Miller said that the team has already used this data to reconstruct the entire ancestral genome "a few times," although the results are still "preliminary."
Estimates for the length of the project vary, with some involved saying it could take as long as two years for a completely assembled ancestral genome to reach the public domain. Other sources involved in the project said an initial draft assembly could be available within the next six months.
Herbolds Donate $1.5M to Bioinformatics Program at Hutch
The Fred Hutchinson Cancer Research Center said last week that philanthropists Bob and Pat Herbold have donated $1.5 million to the center's new program in computational biology and bioinformatics, which is now known as the Herbold Computational Biology Program.
Bob Herbold is the former executive vice president and chief operating officer at Microsoft, where he worked from 1994 until 2003. Before that, he spent 26 years at Procter & Gamble, and he is currently managing director of Herbold Group, a consulting firm.
"The generous support from Bob and Pat will help the Center build one of the best computational biology programs in the world," said Lee Hartwell, president and director of the Hutchinson Center, in a statement.
3rd Millennium Receives SBIR from DOD for Microarray Data-Management System
Bioinformatics consulting firm 3rd Millennium said last week that it has received a Phase II Small Business Innovation Research award from the Department of Defense to develop a bioinformatics platform for the collection, storage, and analysis of microarray data.
The amount of the award was not provided.
The system, called the Array Repository and Data Analysis System (ARDAS), includes a LIMS for managing the laboratory processes and collecting data from both 2-color and Affymetrix arrays; an Analysis Information Management System (AIMS) that includes a workflow engine and computational tools for the statistical analysis of the data; and a data warehouse for storing and organizing both raw and analyzed data sets.
Linguamatics, CGKP Partner on Text-Mining Project
Linguamatics and the Cambridge Genetics Knowledge Park said last week that they are collaborating in a two-year project to mine the scientific literature for gene-disease associations.
Staff at the CGKP will work with Linguamatics to develop the company's I2E natural language processing system for epidemiological applications.
Genedata Licenses Expressionist to Signature Diagnostics
Genedata said last week that it has licensed its Expressionist software to Signature Diagnostics.
The diagnostics company will use the software to identify unique gene expression profiles found in colorectal cancer patients using Affymetrix GeneChip data.
Financial terms of the agreement were not provided.
Formulatrix Licenses Protein Crystallization Software to Novartis
Formulatrix said last week that Novartis has signed a global licensing agreement for the company's Rock Maker protein crystallization software.
The company said that Novartis will use the software to integrate its entire crystallization process, including experimental design, liquid handling, imaging, and data management.
Financial terms of the agreement were not provided.
LANL Hits Milestone with Ribosome Simulation
Researchers at Los Alamos National Laboratory have used the lab's "Q Machine" supercomputer to simulate the behavior of 2.64 million atoms in the ribosome more than six times larger than any biological simulations performed to date, according to LANL.
A paper describing the project was published in the Proceedings of the National Academy of Sciences on Oct. 24.
LANL said that the simulation method should help improve the efficacy of antibiotics, since most antibiotic drugs are less than one one-thousandth the size of the ribosome "and act like a monkey wrench in the machinery of the cell" by diffusing into critical sites of the ribosome and causing it to fail.
The simulations also revealed that transfer RNA must be flexible in two places for decoding to occur.
The simulation was run on 768 of the supercomputer's 8,192 available processors.
Fujifilm to Distribute Decodon's 2D Gel Software in Japan
Fuji Photo Film will distribute Decodon's Delta2D 2D gel analysis software in Japan, the Greifswald, Germany-based company said last week.
Decodon said that the agreement is part of Fujifilm's "strategy to expand life sciences into a core business."
Institut Pasteur Takes Stake in Ariana, Agrees to Use Virtual Screening Software
Ariana Pharmaceuticals said last week that it had signed a "series of agreements" with the Institut Pasteur related to Ariana's new virtual screening platform.
Under the terms of the agreements, Institut Pasteur will take an "unspecified shareholding" in Ariana, and will also license Ariana's virtual screening technology. In addition, the Institut Pasteur will provide Ariana with the use of its Pasteur BioTop incubator.
The financial terms of the agreement were not disclosed.
Ariana's virtual screening platform is based on the company's KEM (Knowledge Extraction Management) technology, which ensures that selected molecules not only have a strong probability of binding to the target but will also have good pharmacokinetic or ADMET qualities, the company said.
DNAPrint Acquires Kenna Technologies
DNAPrint Genomics said last week that it has acquired biological modeling firm Kenna Technologies of West Chester, Pa., in an all-stock deal.
Under terms of the agreement, Kenna's shareholders exchanged all of the company's outstanding shares for 1.5 million shares of DNAPrint Genomics common stock.
"We believe Kenna's technologies will lead to shorter and less expensive drug development times, and represent a powerful tool in our company's search to develop programs for personalized medicine, and test/drug combinations targeting a specific group of patients," said Hector Gomez, chairman and chief medical officer of DNAPrint.
Initially, the Kenna team will support the clinical development of DNAPrint's PT-401 Super EPO erythropoietin dimer for the treatment of anemia and renal failure. Kenna's technology will be used to help design optimal clinical trials with respect to dosing, patient selection factors, and trial duration, DNAPrint said.
DNAPrint has also gained access to Kenna's BoneFusion and CellCycleFusion models through the acquisition. BoneFusion simulates the processes in bone remodeling that underlie diseases like osteoporosis, while CellCycleFusion simulates the molecular pathways that control basic cellular functions.
Equbits Licenses Foresight to Novartis, J&J, BASF
Equbits said last week that it has signed Novartis, Johnson & Johnson PRD, and BASF as the first customers for its Equbits Foresight predictive modeling software.
Financial terms were not disclosed.
Foresight is a desktop and enterprise analytics software package built on support vector machine technology.
Applied InSilico Licenses ELE to GSK
Applied InSilico said last week that GlaxoSmithKline has signed a multi-year agreement for its ELE (Evolutionary Learning Environment) software platform.
Financial details were not disclosed.
ELE is an evolutionary learning and computation system that uses a parallel distributed architecture to enable detailed analysis of large and complex datasets, the company said.
GSK will integrate ELE into a new global decision support environment for library design, model building, and selection of drug candidates. The company will use ELE for automated data analysis and modeling capabilities.
PubGene to Provide Text-Mining Services for Spermatech
PubGene said last week that it will provide customized text-mining services to Spermatech, a biopharmaceutical company focused on the development of agents for the manipulation of sperm movement that can be used as male contraceptives.
PubGene will use its PubGene2.5 text-mining software in the collaboration.
Financial details were not disclosed.