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Columbus, Sybyl, NEAT, Spotfire 2.2, caBIG Life Sciences Distribution, LSD, Life Sciences Distribution version 1.1

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PerkinElmer Life and Analytical Sciences has launched its Columbus high-content screening data management system, a platform for archiving, managing, retrieving, and protecting images and analyzing results for high-content screening experiments.
 
Designed as a partner product for the Opera, PerkinElmer’s confocal microplate imaging reader, the system is compatible with a wide range of image file formats, according to the company. It can be used to archive and manage images from confocal and standard research microscopes, and act as an image repository.
 
The Columbus data management platform utilizes an open protocol, run on the OMERO server developed by the Open Microscopy Environment, a multi-site collaborative effort among academic laboratories and a number of commercial entities that produces open tools to support data management for biological light microscopy. By using an open protocol, the company said the software is interoperable with “a wide variety of instruments and software,” with support being added for more products on a “frequent basis.”
 
The Columbus data management software is available in two versions; Columbus Gallery, which provides data archive, management, and visualization functionalities, and Columbus Conductor, which includes the functionality of Columbus Gallery, plus the ability to analyze or re-analyze HCS data from the Opera imaging reader or other image data using the Acapella image analysis software.
 

 
Tripos International has released its Sybyl suite of computational chemistry and molecular modeling solutions for Mac OS X Leopard.
 
Using applications built into Mac OS X like iChat, Sybyl users can communicate and collaborate with colleagues.
 
The computational power of the Mac, and the ability to utilize multiple processors to speed compute-intensive tasks, is part of the software. To run SYBYL, users need an Intel-based machine running the latest version of Mac OS X Leopard.
 

 
DxTerity Diagnostics has released the NEAT probe design software. Developed in conjunction with Premier Biosoft International, NEAT is included within Premier Biosoft's Allele ID 7.0 platform.
 
NEAT replaces enzymatic amplification techniques with a chemical reaction and, according to the company, will help propel the development of “affordable genomic tests” in areas such as point-of-care testing or live cell assays.
 
The software module is built within the framework of Allele ID, which lets users tailor the platform to their needs. The program can be used to design multiplexed, quantitative mRNA and miRNA expression assays as well as mutation detection assays.
 

Tibco Software has released Spotfire version 2.2, which includes 3D visualizations, network visualizations, and tools to help scientists and businesspeople use interactive data visualization, including a new feature called Spotfire Network Analytics. According to a statement, the new software allows business professionals to explore relationships between different types of data.  
 
In addition, Tibco introduced the Tibco Spotfire Technology Network, an online resource for developers who are using the Spotfire Software Development Kit to extend and adapt the market’s leading interactive visualization experience to their business needs.
 
Tibco Spotfire 2.2 allows users to analyze complex multi-dimensional data by zooming and rotating in three dimensions to analyze their data and spot hidden patterns.
 
Spotfire Network Analytics complements Spotfire 2.2 in that it offers interactive visualizations of data relationships, allowing users to explore the network of relationships between data that is otherwise hidden. 
 
As a resource for developers and technologists, for example, to access the Spotfire Software Development Kit and APIs to adapt the platform, TIBCO has launched Spotfire Technology Network, available here.  
 

 
The National Cancer Institute Center for Bioinformatics has released version 1.1 of the Life Sciences Distribution, or LSD, for theCancer Biomedical Informatics Grid.
 
This set of tools supports various aspects of research, from tracking and managing biospecimens to analyzing and integrating microarray data. The bundle’s components are:  
  • geWorkbench version 1.6: A platform for genomic data analysis, visualization and annotation of microarray-based gene expression and sequence data, available here
  • Life Science Distribution Browser, LSDB, version 1.0: A web-based search tool for keyword searches on local or remote grid-enabled LSD services. This first release of LSDB supports searching across the National Cancer Imaging Archive and caArray. Available here
  • caArray version 2.1.1: This version of NCI’s array data management software, which connects with other tools such as geWorkbench is available here
  • National Cancer Imaging Archive, NCIA, version 4.0: The NCI’s repository for DICOM, or Digital Imaging and Communications in Medicin, standard-based images is available here: and the Medical Imaging Resource Center data submission software is available here
  • Clinical Trials Object Database Systems, CTODS, version 1.0: A repository for identifiable and de-identified clinical trial information and which includes data loading scripts, available here.
  • caGWAS version 1.0.1: A version of the NCI’s caIntegrator platform that supports Genome Wide Association Studies such as the Cancer Genetic Models of Susceptibility (CGEMS) data, available here.  
  • caTissue Core version 1.2.2: A caGrid-enabled version of the caTissue Core application, available here
According to a caBIG statement, each tool has a graphical user interface and each of the data management tools has a Java-based API, and a caGrid compatible Grid Service to allow programmatic access to data.
 
All of the applications are open source and components of this bundle can be downloaded here.   
 

Additional information is available here.

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