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Downloads and Upgrades: Apr 15, 2011

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This week, Gene Logic, an Ocimum Biosolutions company, announced that licenses for its Ascenta 4.0 analysis system are now available at a special price to all academic and non-profit organizations.

Ascenta is web-based system that was developed to simplify access to and information retrieval from BioExpress, Gene Logic’s proprietary gene expression database. The tool enables researchers to identify and prioritize drug targets and biomarkers across multiple disease and tissue settings.

The company said the latest version of Ascenta incorporates more data and improved features that help researchers study and analyze their genes of interest.


Biomatters has released Geneious Server 1.1. The latest release adds several new algorithms and improved capabilities to help researchers offload high-intensity processing to computer clusters straight from their desktops.

With the changes, researchers can launch LastZ, Glimmer, PAUP* and SOAP2 algorithms from their desktops to run on Geneious Server or schedule them to run on high-performance computing clusters. Furthermore, the release now supports Platform Computing's LSF cluster workload manager.


Scilligence has launched three new software products: Open Lab Notebook, Chem4SharePoint, and JSDraw.

OLN is a web-based electronic lab notebook that lets users record, organize, and analyze experimental information on a computer as well as draw, display, and search chemical structures. Users can also access OLN from any computer including iPad and Android tablets via a web browser. Chem4SharePoint lets users draw, display, and search chemical structures in Microsoft SharePoint. JSDraw is a javascript chemical structure editor and viewer that lets users draw and display chemical structures


Dotmatics has integrated Lexichem, an automatic chemical naming tool from OpenEye Scientific Software, into Studies Notebook, Dotmatics' electronic laboratory notebook solution.

Integrating Lexichem's naming functionality to Studies Notebook allows scientists to have all of their reactions, products, and reagents automatically named in the conventional IUPAC format. Studies Notebook provides a web-based platform for both chemistry and biology electronic data capture in discovery research.


Simulations Plus has released MedChem Studio 2.0

The new release includes MedChem Designer, a molecule drawing tool; additional multidimensional graphics output; enhanced import capabilities for molecular structure files; and enhanced capabilities for exporting results among other features.


ChemAxon has launched JChem for SharePoint to enable chemistry within Microsoft’s SharePoint platform. The launch includes web parts, which are functionality sections that can be inserted into pages in SharePoint sites, and custom lists for chemical editing, search, and property prediction.

JChem is a chemical platform toolkit that enables life science researchers to store, search, and characterize chemical structures. The parts and custom lists let users add enterprise chemistry understanding to SharePoint intranet portals, extranets, websites, blogs, wikis, and other SharePoint instances.


This week, the Allen Institute for Brain Science released a human brain map, which serves as the foundation for the Allen Human Brain Atlas, an online public resource developed to advance the institute’s goal to understand the human brain.

The atlas identifies 1,000 anatomical sites in the human brain, backed by more than 100 million data points that indicate the particular gene expression and underlying biochemistry of each site. Scientists can use the tool to explore the human brain and identify how disease and trauma, including physical brain injuries and mental health disorders, affect specific areas of the brain.

The atlas incorporates data from magnetic resonance imaging, diffusion tensor imaging, as well as histology and gene expression data derived from both microarray and in situ hybridization approaches.


Elsevier, the European Molecular Biology Laboratory, and the University of Copenhagen have launched Reflect-Network on SciVerse Applications beta.

The application is integrated within life sciences journals on SciVerse Science Direct via Reflect, a tool that tags proteins and chemicals in a document. It recognizes genes, proteins, and chemicals mentioned in ScienceDirect articles and generates a graphical representation displaying the interactions between the entities. Researchers can then link to the STITCH network to obtain additional details about entities and different ways to view the network such as color-coded lines revealing modes of action, or drill down to examine the evidence supporting each interaction.


Tripos has released Discovery 360 version 5.5.

The release provides new automation, communication, and data visualization capabilities to assist scientists in their data workflows.

It enables automated data manipulations, analysis, and dataset visualization, and includes annotation tools so that users can share their progress on experiments with project teams, among other features.


GenBank 183.0 is available via FTP from the National Center for Biotechnology Information.

Uncompressed version 183.0 flatfiles require roughly 489 gigabytes for sequence files only or 530 gigabytes to include the short directory, index, and text files. The ASN.1 data require approximately 402 gigabytes.


Bioconductor 2.8 is available here.

The release consists of 466 software packages and more than 500 up-to-date annotation packages including 48 new software packages and improvements to existing packages.


The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.