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Downloads and Upgrades: GenBank 194.0, OpenEye Toolkits, JCB DataViewer, and more

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GenBank 194.0 is now available via FTP from the National Center for Biotechnology Information.

Uncompressed flatfiles for 194.0 require roughly 587 GB for sequence files only
or 632 GB to include the short directory, index, and text files. The ASN.1 data require approximately 481 GB.


OpenEye has released OpenEye Toolkits v2013.Feb.

This release includes the C++, Python, .NET, and Java versions of the toolkits.

The full release notes are available here.

The toolkits can be downloaded here.


Certara's Simcyp said this week that it has released a pregnancy model for its simulator platform, which is used for quantitative prediction of drug-drug interactions and pharmacokinetic-pharmacodynamic outcomes in virtual populations.

The pregnancy model enables physiologically based pharmacokinetic modeling of concentration-time profiles of drugs in pregnant women in a way that accounts for the physiological and anatomical changes that happen during gestation. The company also provides a pregnancy population library that contains known changes that influence how drugs are handled throughout the different stages of pregnancy.

Simcyp has also released a scripting facility that lets users customize pharmacodynamic response models.


This week, Real Time Genomics launched a genome analysis platform that is compatible with data from sequencers marketed by Illumina, Life Technologies' Ion Torrent, Roche's 454, and Pacific Biosciences.

The company said that its platform takes raw sequence data, aligns it to a reference genome, and then it detects variants such as SNPs, small insertions and deletions, and structural variants. So far, it said, it has used the system to identify disease-causing variants associated with early neurodevelopmental childhood disorders and neonatal diseases.


Glencoe Software and the Journal of Cell Biology have updated the JCB DataViewer, a tool for presenting, sharing, and archiving published scientific image data.

This release includes updates in the design and layout of the JCB DataViewer that improves access to and the use of complex multi-dimensional image datasets associated with papers published in JCB. It also includes workflow improvements; streamlined upload for authors; and improved presentation of large, complex datasets from high content screening and large tiled arrays.


The Scan

Call for a Different Tack

Experts weigh the value of recent experiments testing genetically modified pig kidneys using brain-dead individuals, according to Nature News.

Wastewater Warning

The New York Times reports that wastewater surveillance in some parts of the US point to a possible surge.

Can't Get in the Program

Due to the Northern Ireland protocol dispute, the European Union is preventing UK researchers from joining the Horizon Europe research program, the Times of London reports.

Science Paper on Spatial-Controlled Genome Editing

In Science this week: approach to enable a CRISPR-Cas13a-based system to be used as a cancer therapy.