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Tripos, Accenture, Wyeth, European Bioinformatics Institute, Centre for Ecology & Hydrology, GenoLogics, Dana Farber Cancer Institute, Oracle, Bayer CropScience, Ariadne, University of Nevada, Windber Research Institute, Tepnel, SoftGenetics

Tripos, Accenture Roll Out Discovery 360 Implementation at Wyeth
BOSTON — Tripos this week said that it has completed a two-year project to implement an integrated discovery research informatics platform at Wyeth Research based on the Tripos Benchware Discovery 360 system.
Tripos officials announced the roll-out of the platform, which the company deployed in collaboration with consulting firm Accenture, at IBC’s Drug Discovery & Development of Innovative Therapeutics conference held here this week.
The platform integrates new and legacy data repositories at Wyeth and enables the company’s scientists to access, analyze, and share enterprise-wide research data from a single “hub,” Patrick Flanagan, senior vice president of business development, told BioInform.
He added that the system “minimizes the time it takes researchers to collect information,” and “leverages the global scale” of a large organization like Wyeth.
So far, 250 Wyeth scientists have been trained on Benchware Discovery 360, and the system will be deployed to all of the pharma’s 1,200 discovery scientists by the end of the year, Tripos said.
"This is an important milestone in our efforts to enhance and streamline the way we access, use, and share the data generated by our discovery research scientists," Frank Walsh, executive vice president of discovery at Wyeth Research, said in a statement.
Flanagan said that Accenture is currently working with Wyeth researchers to quantify the return on investment from the platform, which has undergone a number of iterations since the project kicked off more than two years ago.
When Wyeth tapped Tripos for the project in 2006, estimated to be worth around $5 million at the time, the informatics company planned to use the SMART-IDEA (Structure Modeling Analysis Research Tool Integrating Data for Experimental Analysis) integration platform that it had developed in collaboration with Accenture for Bristol-Myers Squibb in 2002 [BioInform 01-13-06].  
Later that year, Tripos took steps to “productize” the SMART-IDEA technology under the Discovery 360 name as part of a strategy to expand its Benchware line of products [BioInform 08-11-06]. 
In 2007, the publicly traded Tripos sold off its Discovery Research business to Commonwealth Bio, sold its Discovery Informatics business to buyout boutique Vector Capital for $26 million, and liquidated its remaining assets.
With Vector’s support, the informatics group remained in business as a privately held firm and retained the Tripos name. The company renegotiated the timeline for the Wyeth contract, which had lagged as a result of the restructuring.
Flanagan said that the completion of the Wyeth project is an important “validation of the platform” and also “validates the roadmap we’re taking.”
He said that the company is in discussions with other potential customers for the Discovery 360 system, and that while the firm hopes to “find another Wyeth,” it is also looking into developing a “lighter, nimbler” version of the platform that would be targeted at smaller research groups.

Community Initiative Launches to Harmonize 'Minimum Information' Checklists
More than 20 molecular biology standardization groups have launched a joint initiative to coordinate a growing number of so-called “minimum information” checklists that have been created to assist scientists with data sharing and integration from genomics, proteomics, and other high-throughput biological experiments.
The initiative is called the Minimum Information about a Biomedical or Biological Investigation project, or MIBBI.   
In a commentary in the August issue of Nature Biotechnology, a group of 58 researchers, led by the European Bioinformatics Institute and the UK’s Centre for Ecology & Hydrology, describe the harmonization effort, which aims to provide an overarching set of guidelines for standardization groups to ensure interoperability and prevent duplication of effort.
The initiative offers a web and community-based resource to foster, as the scientists wrote, “collaborative, integrative development of checklists.”
Since the publication in 2001 of the first minimum information checklist, “Minimum Information About a Microarray Experiment,” or MIAME, a number of projects have formed to create similar guidelines for reporting data about data, or metadata, generated in different biological experiments and on various instruments.
However, this proliferation of projects presented a challenge because “different communities were at risk of developing mutually incompatible standards,” Chris Taylor, a researcher at the European Bioinformatics Institute and co-author of the Nature Biotech paper, said in a statement.
In addition, the authors note in the paper, “overlaps in scope and arbitrary decisions on wording and substructuring [for different checklists] inhibit their use in combination” — an issue of particular concern for researchers who “routinely combine information from several disciplines.”
As a result, several existing checklist projects formed MIBBI in an effort to “facilitate the development of an integrated checklist resource site for the wider bioscience community,” the authors wrote.
To date, 21 checklist development projects have registered with MIBBI, including MIAME, MIAPE (Minimum Information about a Proteomics experiment), MIARE (Minimum Information about an RNA interference Experiment), MIGS (Minimum Information about a Genome Sequence), MIACA (Minimum Information about a Cellular Assay), and MIRIAM (Minimum Information Requested In the Annotation of biochemical Models).
“Communities working together through MIBBI will produce non-overlapping minimal information modules,” said Dawn Field, a researcher at the UK’s Natural Environment Research Council Environmental Bioinformatics Center and a co-author of the paper. “The idea is that each checklist will fit neatly into a jigsaw, with each community being able to take the pieces that are relevant to them.”
The first part of MIBBI is the MIBBI Portal, which provides summary information for each of the registered projects and exists “simply to raise awareness of, and afford more straightforward access to, a wide range of checklists by providing researchers, journal editors, reviewers, funders and the wider community of checklist developers with a quick and simple way to discover (whether there is) a checklist addressing a particular area and to establish the scope and progress of the underlying project,” according to the paper.  
The second component of the project is the MIBBI Foundry, which also has a wiki, and which plans to closely examine the available checklists and eventually develop a suite of “self-consistent, clearly bounded, orthogonal, integrable checklist modules.” The foundry, the authors note, is modeled on the Open Biomedical Ontologies Foundry for ontology development.
“MIBBI represents the first new effort taking the Open Biomedical Ontologies (OBO) as its role model”, said EBI researcher Susanna-Assunta Sansone in a statement. “The MIBBI Portal operates in a manner analogous to OBO as an open information resource, while the MIBBI Foundry fosters collaborative development and integration of checklists into self-contained modules just like the OBO Foundry does for the ontologies.” 
These modules will be released through MICheckout, a tool that is currently under development by the EBI and the NERC’s Environmental Bioinformatics Center. MICheckout will assist users in compiling the correct list of modules and downloading them in a form that they can use, the paper said.

Dana-Farber Cancer Institute Deploys Oracle for Clinical and Research Data
Dana-Farber Cancer Institute is installing Oracle’s Healthcare Transaction Base and Oracle Fusion Middleware components to shape its new translational research infrastructure.
According to a statement, Dana-Farber has large amounts of patient and clinical data as well as thousands of biological samples that it is seeking to leverage for improved disease understanding and patient care.
As part of designing new studies and addressing complex questions, researchers want to aggregate clinical, sample, and genomic data from within and beyond the organization's collections, Oracle said.
Using Oracle Healthcare Transaction Base, Dana-Farber has created an integrated data repository that enables researchers to access clinical and sample data using a single platform and connect it with experimental data.
This data infrastructure helps researchers investigate clinical data, query it in more complex ways than previously possible, and obtain quicker answers, according to a statement. The institute also deployed Oracle Identity Management and Oracle Access Manager, which are components of the Oracle Fusion Middleware suite, to let researchers securely access data from any location.
Oracle Fusion Middleware is used to build and manage web services that facilitate integration with third-party applications for advanced analytics and data mining across the various data sets.
This infrastructure is “helping us to maximize the use of this information in our quest to develop a better understanding of and treatments for serious diseases," John Quackenbush, professor of biostatics and computational biology at Dana-Farber, said in a statement. The system, he said, "is scalable and extensible, and one that can serve as a framework for other organizations facing similar challenges."

Bayer CropScience Licenses Ariadne Pathway Studio
Ariadne announced that Bayer CropScience has licensed its Pathway Studio platform, including the ResNet Plant database, to supplement its plant stress reactions research.
According to a statement, the company will use Pathway Studio for gene expression analysis of plant and fungi data.
Pathway Studio is equipped with an information extraction module that helps scientists to customize Ariadne’s standard databases such as ResNet Mammalian and ResNet Plant and helps them create new databases for particular research topics or species, the company said.
Ariadne also reported that Bayer CropScience licensed Metabolic Vision, a bacterial and fungal pathway database by Integrated Genomics and distributed by Ariadne, which is compatible with Pathway Studio.

GenoLogics Sells Informatics Systems to Nevada, Windber Institutes
GenoLogics has reached a joint development agreement with the University of Nevada and it is collaborating with the Windber Research Institute to develop an integrated platform using the company’s Biomedical Informatics suite, the company said this week in separate announcements.
GenoLogics said it is working with the University of Nevada’s Proteomics Center, a core facility that provides high-throughput proteomic and metabolomic services to Nevada’s researchers, to deploy its Proteus centralized data management system.
This system lets scientists in a lab aggregate data from several technology platforms and pull them together through the LIMS for analysis. Proteus enables secure collaboration through an online communication interface called LabLink, the company said.
The Windber Research Institute, meanwhile, is using the company’s software to integrate tissue banking data and patient sample annotation with molecular and imaging data to enhance clinical practice. The agreement builds on a previous collaboration that GenoLogics and Windber entered in October 2007 [BioInform 10-26-07]. 
The company’s Biomedical Informatics suite helps scientists and clinicians manage biospecimens and clinical annotations, process queries and sample requests, offers tools for enabling web access, study management, and handling electronic patient questionnaires.
Windber Research Institute CSO Richard Mural said the informatics solution “will allow us to integrate both discovery and clinical data into a single system for a holistic view, which is necessary to pursue the type of research we are doing.”
No financial terms of either agreement were released.

Synamatix Joins Illumina Connect Program
Kuala Lumpur-based Synamatix said this week that it has become a member of the Illumina Connect program, which provides Illumina customers with access to data-analysis applications for the company’s Genome Analyzer.
The focus of the collaboration is to leverage the recently launched SynaWorks, a bioinformatics package for next generation sequencers, Synamatix said.

Tepnel to Distribute SoftGenetics Software with Trisomal Dx Kits
British medical diagnostics company Tepnel Life Sciences will market and distribute SoftGenetics’ genotyping software for use with its prenatal screening test, Tepnel said this week.
Under the agreement, Tepnel will market the GeneMarker software with its Elucigene QST*R kits, which are rapid DNA diagnostic tests that use STR markers to detect three common trisomal disorders, including Down syndrome, Edwards syndrome, and Patau syndrome.
Using the GeneMarker software with the kits “will considerably streamline the data analysis process and results reporting time for users,” Tepnel said.
Tepnel is based in Manchester, UK, and it has laboratories in the US and in France. It provides tests and reagents for molecular diagnostics and biomedical research.
SoftGenetics has facilities in Stamford, Conn., and in State College, Pa., and it focuses on developing software for research and diagnostic applications.
Financial terms of the agreement were not released.

Symyx to Integrate OpenEye Tools with Symyx Draw, Isentris 3.1
Symyx Technologies said this week that it plans to integrate OpenEye Software’s Lexichem structure-name converter software with Symyx Draw and other solutions including the soon-to-be-released Symyx Isentris 3.1 informatics system.
This integration will help chemists with chemical compound searching and structure creation, Symyx said.
As part of this agreement, Prous Science, which belongs to the scientific business of Thomson Reuters, and Symyx are extending to OpenEye access to the MDDR database, a bioactivity database jointly produced by Symyx and Thomson Reuters, for use in validating OpenEye’s various scientific algorithms. OpenEye will also be able to validate its models against the Symyx Comprehensive Medicinal Chemistry database, the company said. 

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