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Downloads and Upgrades: Certara's Phoenix; TopHat 2.0.0; CLC Bio


Certara has released a new version of Phoenix, its pharmacokinetic/pharmacodynamic modeling software platform.

Version 1.3 includes updates to several Certara products including Phoenix WinNonlin 6.3; Phoenix NLME 1.2; Phoenix Connect 1.3; AutoPilot Toolkit 2.1 for Phoenix; and IVIVC Toolkit 2.1 for Phoenix WinNonlin

These updates include an improved sampling method for the Quasi-Random Parametric Expectation Maximization algorithm in Phoenix NLME; increased support for developing integrated workflows that include algorithms from third-party software in Phoenix Connect; the ability to execute third-party compute jobs on a high-performance compute cluster through a remote processing server; and other changes.

The Center for Bioinformatics and Computational Biology at the University of Maryland has released TopHat 2.0.0.

The release supports Bowtie 2 and provides improved parallelization and the ability to align RNA sequencing reads across potential fusion points, among other updates.

CLC Bio no longer offers three desktop software packages: CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench.

The features from these three products have been incorporated into the CLC Main Workbench for sequence analysis and gene expression analysis.

The company has also lowered the price of the CLC Main Workbench from $3,950 to $1,999 for industrial customers and from $985 to $399 for academic customers for static single computer licenses. Network licenses now cost $3,999 and $799 for industry and academia, respectively.

The company has also added a limited-term $179 price reduction for the workbench for academic researchers that will last until May 31.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.