news
Geneious Biocode LIMS made freely available
The Laboratory Information Management System (LIMS) developed for the Moorea Biocode Project is to be made publicly available as a free beta version. The Biocode LIMS and data analysis components of the project were developed by Biomatters in collaboration with the Biocode Project researchers as a plugin for Biomatters’ Geneious Pro sequence analysis software.
The Geneious Biocode LIMS will give biologists around the world a tool to use in their own research, as well as access to the Moorea project’s fi nal database. An accompanying ‘Biocode Genbank Submission’ plugin will allow researchers to upload their own sequence data from inside Geneious Pro directly to Genbank, the world’s largest public DNA sequence database. The Biocode LIMS system provides an informatics pipeline for batch processing of samples from DNA extraction through to sequencing, identifying and re-running failed reactions, and identifying systematic errors that can be strategically
including the completely tracked history. Neil Davies, director of UC
Human DNA extracted from blood
addressed. It integrates with Geneious Pro’s existing sequence assembly tools and various Field Information Management Systems (FIMS), including TAPIR standard access protocols. Once the specimen reaches the end of the pipeline, the Biocode Genbank
submission plugin automates the submission of completed contigs to make the DNA sequences publically available. The reaction data from the LIMS database is combined with the fi eld metadata from the FIMS database as a quality control mechanism
Princeton Mass Spectrometry Center buys licence for Integromics’ OmicsHub
Integromics, a provider of IT solutions for life sciences in the fi eld of genomics and proteomics, has announced that the Princeton Mass Spectrometry Center has purchased a licence for the Integromics’ OmicsHub Proteomics solution. Integromics will deploy the solution and create a functional data analysis infrastructure by the end of 2010, whereby Princeton will use it as a key element in its strategy for data management and analysis of mass spectrometry (MS) data. For a rapidly growing MS centre such as the one at Princeton, tracking, administering, analysing and performing large numbers of IT tasks on signifi cant amounts of MS data is a vast undertaking that can become prohibitively elaborate. These activities quickly become a bottleneck to research, limiting the speed or the depth of the data analysis that can be performed routinely. OmicsHub will help the facility to continually engage in large numbers of collaborative MS
www.scientific-computing.com AS WE BECOME ONE
OF THE PREEMINENT SCIENTIFIC COLLABORATIVE RESEARCH CENTRES FOR MS AND SYSTEMS BIOLOGY, THE AMOUNT OF DATA THAT WE PRODUCE, ANALYSE AND MANAGE IS DAUNTING
projects of increasing complexity. Currently in the MS marketplace there are separate solutions for data management and analysis. OmicsHub provides a global solution that integrates both of these into a single platform, streamlining the data analysis workfl ow, increasing effi ciency and productivity, saving time and money, and facilitating collaboration between scientists.
‘As we move to become one of the pre-eminent scientifi c collaborative research centres for mass spectrometry and systems biology, the amount of data that we produce, analyse and manage is daunting. We believe that Integromics’ comprehensive OmicsHub solution will play a critical role in our successful strategy to address this and establish an effi cient infrastructure necessary for large-scale projects and systems-wide informatics,’ said David Perlman, director of the Princeton Mass Spectrometry Center. OmicsHub was developed by Integromics as a result of a collaboration with the Spanish National Institute for Proteomics (ProteoRed) and the Proteome Xchange. The comprehensive data management tool allows the user to collect, annotate and conduct qualitative and quantitative analysis of mass spectrometry data.
Berkeley’s Gump South Pacifi c Research Station and principal investigator of the Biocode Project said: ‘This is the fi rst freely available, broadly applicable software tool to assist tracking materials through the DNA barcoding pipeline. No other freely available program allows the level of tracking and data quality assurance through a lab system. Importantly, it goes beyond DNA barcoding to accommodate multiple genetic markers for use in a broad range of biodiversity and ecogenomic studies. ‘The plate workfl ow approach taken has greatly simplifi ed the process of identifying reaction failures, and setting them up to be run again. It manages data that used to be spread across multiple individuals and notebooks so we can search it, report success, or look for patterns. It has signifi cantly reduced the human error that has been problematic in large-scale sequencing projects such as this in the past,’ he added.
IN BRIEF
Ingenuity Systems and CLC bio have announced they are collaborating to provide interoperability between their software solutions. A partnership between Biomatters and Active Motif will lead to faster sequence analyses for researchers with high-intensity visualisation and computing needs. Biogemma has selected Tibco Spotfi re 3.1 to move beyond transcriptomic analyses and embark on new types of integrative research based on genetic maps. Panasas has announced the appointments of Bill Ribera to vice president of worldwide sales and Celeste Baranski to senior vice president of engineering. UK-based software company Nonlinear Dynamics has expanded its sales team through the creation of two new senior positions in the US and Europe.
FEBRUARY/MARCH 2011 5
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