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Bio-IT World: Illumina, Next Bio, BGI, Others Launch New Informatics Products


A roundup of new product offerings announced at the annual Bio-IT World conference held this week in Boston, Mass.

Illumina introduced BaseSpace Apps, a dedicated application store for BaseSpace, the genomics cloud computing platform that the company launched last year (BI 10/14/2011).

Informatics solutions available through BaseSpace Apps will allow customers to connect with a community of academic, commercial, and open source tool providers who are building genomic analysis applications for Illumina data.

BaseSpace Apps also includes a publicly available application programming interface that allows developers to create and deploy new applications. Currently the sequencing vendor has tapped Diagnomics, GenoLogics Life Sciences, Genomatix, Golden Helix, Ingenuity Systems, Knome, Omicia, Spiral Genetics, Omixon, Real Time Genomics, Station X, Integromics, Biomax Informatics, and Strand Life Sciences as initial application development partners.

Illumina also introduced its iSAAC genome alignment tool, which is available on BaseSpace as well as standard workstations. The company claims that iSAAC maps sequencing reads to their proper locations up to 10 times faster than existing aligners.

Finally, Illumina also released the MyGenome app, which enables users to explore a real human genome and view reports about genetic variations on their iPads.

NextBio launched NextBio Clinical, a version of the company’s existing life sciences platform that supports translational medicine applications such as biomarker discovery and clinical trial optimization.

According to the company, the new platform adds curated genomic, molecular, and clinical profiles from thousands of individual patients to an existing repository of data from animal and cell line models. It aggregates and correlates private and public 'omics data, experimental data from cell lines and other sources, and clinical data from individual patients and population studies, NextBio said.

Saeid Akhtari, NextBio’s president and CEO, said in a statement that NextBio Clinical is a “natural extension” of its existing life science platform.

At the American Society of Human Genetics meeting last October, the company released the results of two in-house studies it performed to provide proof of its ability to help pharma and clinical researchers mine publicly available genomic data in their translational research efforts — one that explored the biological mechanisms involved in the toxicity of tibolone, a hormone replacement therapy for post menopausal women; and a second study in which the company's researchers found a potential cancer biomarker by analyzing publicly available data (BI 10/28/2011).

Akhtari said this week that the release enables the company to “directly address the challenges of taking genomics into clinical research for the development of therapeutics and companion diagnostics” by providing “patient-centric data and analysis.”

BGI launched EasyGenomics, a cloud-based software-as-a-service solution for next-generation sequence data analysis.

BGI said that platform provides workflows for whole-genome resequencing, exome resequencing, RNA-seq, and small RNA sequencing. It also provides a de novo assembly workflow based on the Apache Hadoop MapReduce distributed computing framework.

The platform also includes back-end databases that are used to store datasets and a resource management engine that lets users distribute and monitor computational tasks.

In addition, EasyGenomics integrates Aspera’s fasp high-speed file transferring technology and Connect server solutions.

Aspera's Connect server enables high-speed sequencing data import/export, while the fasp solution is integrated directly into the web portal using application programming interfaces that are available through the Aspera Developer Network.

EasyGenomics also includes Nvidia graphics processing units, which speed the processing of the analysis of sequence data from days to hours compared with CPU-based systems, Nvidia said.

Specifically, the EasyGenomics cloud service features hybrid computing systems powered by Nvidia Tesla M2070 and M2075 GPUs, which accelerate the DNA sequencing data analysis in conjunction with system CPUs.

Additionally, BGI plans to upgrade the EasyGenomics service with hundreds of additional Tesla GPUs when it is fully deployed, at which time it is expected to support thousands of users, the hardware vendor said.

Thomson Reuters launched its Partner Ecosystem through which third-party developers can build applications that provide access to life science data in its Cortellis platform.

Thomson Reuters launched Cortellis — a web service that provides access to all its drug research and development content via a single platform — last November. In March, the company launched Cortellis for Informatics — a set of application programming interfaces that lets researchers combine information from the company’s commercial drug development databases with their own internal data as well as information from public sources (BI 3/2/2012).

According to the company, third-party developers can now use the Cortellis open architecture to access Thomson Reuters’ content and technology and create customized solutions for their customers.

As part of the Partner Ecosystem program, the data vendor provides ontologies, biological target information, and other data that supports pharmaceutical business development and competitive intelligence projects.

Participants in the ecosystem will also have access to the Cortellis developer center, a forum for sharing ideas and best practices and discussing new applications. The developer center also provides access to technical support from Thomson Reuters.

So far, the company has partnered with IDBS to integrate its E-Workbook with Thomson Reuters Cortellis.

Specifically, the companies have integrated their solutions through ScienceLink, a feature of IDBS’ ELN, which lets researchers access content from Thomson Reuters’ Integrity using the Cortellis for Informatics Targets API directly within E-WorkBook.

The combined solution lets research teams search literature and curated sources and integrate all their available knowledge. The partners expect the combined solution to be of use in target identification and validation, experimental pharmacology, toxicology, and biomarker discovery.

IDBS has also updated its ChemBook electronic laboratory notebook with the addition of ChemAxon’s reactor engine — known as the Parallel Synthesis add-on — which is used to support chemists’ workflows and synthesize libraries of compounds in a parallel fashion.

ChemAxon’s reactor lets chemists define a generic reaction, a set of reactant structures, and combine the two to enumerate and iteratively tune a set of product compounds and discrete reactions.

Users can draw and edit reactants directly as well as run and tune reactions. IDBS ChemBook user interface ensures that all intellectual property is captured and stored in-house, the company said.

At the conference, IDBS was showcasing its enterprise platform — which supports its E-Workbook as well as applications for chemical and biopharmaceutical research, translational medicine, and NGS. It also highlighted its new browser and tablet versions of E-Workbook, which provide customers with multiple interfaces through which they can visualize and search the same enterprise data in a single product.

Neil Kipling, IDBS CEO and founder, said in a statement that the company's partnerships with Thomson Reuters and ChemAxon will enable scientists to use “real-world clinical data in a secure framework alongside research data.”

Partek released an updated version of its Partek Flow software, the company’s next generation sequence data analysis solution, which includes some new enhancements and features.

The updated tool now includes the company’s algorithm for transcriptome analysis, which applies multiple models to each transcript to identify the best analysis fit. The algorithm won the most creative algorithm in the Illumina iDEA challenge last year (BI 7/1/2011).

Dotmatics launched a new chemistry add-in for Microsoft Office.

The software, dubbed Dotmatics for Office, enables scientists to import, create, and modify scientific data in Microsoft Excel, Word, Outlook, and PowerPoint as well as move data between applications. The software is also integrated with Dotmatics’ Browser — a web-based query and reporting solution — which allows the add-in to incorporate data from multiple databases in an Office document.

Furthermore, users can perform structure searches and scientific property calculations within Office applications. Information can be shown in a variety of formats chosen by the user, or according to predefined templates. Further analysis can be carried out within the company's Vortex data visualization and analysis solution.

Mike Hartshorn, director and CSO of Dotmatics, said in a statement that his firm’s new offering "will enable scientists to uncover and retrieve data” stored in things like corporate registration databases and electronic notebooks and move it into “user-friendly Office applications.”

This should help prevent “transcription errors, uncover trends and, ultimately, expedite research," he added.

The tranSMART project released the first open source version of the tranSMART software for translational research.

The platform is now broadly available to institutions looking for an open framework for integrating and sharing data across medical records, clinical trials, reference content, and 'omics data.

It is the product of multiple collaborations between non-profits, academic medical centers, pharmaceutical companies, and commercial groups. These include Sage Bionetworks, the CHDI Foundation, and Janssen Research & Development. On the academic front, contributors include the University of Michigan and Imperial College London

The tranSMART software was internally developed as a translational research data repository for Janssen R&D, which decided to move it to an open source model in December 2011. The primary features for data analysis were produced as an extension of the open source Informatics for Integrating Biology and the Bedside, or i2b2, software, with specific adaptations and extensions to provide researchers with workflows in drug discovery and pharmaceutical R&D.

Version 1.0 includes a major update to the framework, including an upgrade to leverage i2b2 1.6; a plug-in environment for R-based analytics, new correlation analysis algorithms, and new multi-modal data export utilities.

In addition to the release, the project team has established an online presence for open source developers and scientists to contribute to the platform.

Meanwhile, Recombinant Data will offer services for the tranSMART platform, the company said this week.

Recombinant Professional Open Source Services for tranSMART include: performance tuning and system audit; installation and testing of application updates and patches; technical support; and end user training and educational materials among other services.