Skip to main content
Premium Trial:

Request an Annual Quote

Beacon Designer, MutaPrimer, AGOS, PharmaPendium, Scalable HMMer, Tandy Herren, Neil Kabrun, Michelle Gordon-Savenor


Downloads & Upgrades

Premier Biosoft has released version 5.10 of Beacon Designer, an oligo-design tool for real time qRT-PCR. The new version includes improved support for multiplexing. Beacon Designer can design SYBR Green primers, TaqMan probes, LNA-spiked TaqMan probes, FRET probes or molecular beacons for real time qRT-PCR, and NASBA assays, the company said. According to the company, Beacon Designer designs primers by avoiding regions of significant homology, which the software identifies by automatically interpreting Blast search results.

Premier Biosoft has also released MutaPrimer, a free desktop tool to design mutagenic primers for Stratagene's QuikChange site-directed mutagenesis kits, at

The Laboratory of Computational Physiology at the Universidade Federal de Juiz de Fora in Brazil has released a web portal for AGOS, an online tool that builds up an object-oriented C++ class library that allows users to manipulate and numerically solve Initial Value Problems based on ODE systems described by the CellML standard. The AGOS portal is available at

Elsevier MDL has released PharmaPendium, an online database of drug safety information, at PharmaPendium offers searchable access to FDA Approval Packages as well as a longitudinal view of preclinical, clinical, and post-market safety data. Drug safety information can be queried by drug class, by adverse effect/toxicity, by target, and by chemical structure.

Scalable Informatics has released Scalable HMMer, an accelerated implementation of the HMMer algorithm, at Binaries and patches are licensed under the GPL v2.0, and commercial licensing and support are also available for internal use as well as for distribution purposes. According to Scalable, the accelerated version offers up to 2.5-fold speedup over the binary code available at the HMMer website.


People in the News

DNAPrint Genomics has named Tandy Herren director of simulation technology and Neil Kabrun director of biological modeling. Herren will be responsible for applying DNAPrint's BioFusion simulation technology and other modeling techniques to support the company's drug and diagnostics development programs. Kabrun will be responsible for "the acquisition and implementation of a toolbox of techniques and systems that will continue to advance the role of computational methods in improving product development," the company said in a statement.

Herren was formerly a scientist at Kenna Technologies, which DNAPrint acquired last November. Kabrun served as an independent consultant before joining DNAPrint. Prior to that, he held computational biology positions at Transgenomic and Genomica.

Genstruct has appointed Michelle Gordon-Savenor as director of alliance management, a role in which she will be responsible for managing the alliances between Genstruct and its pharmaceutical partners, including Schering and Pfizer. Gordon-Savenor was previously alliance manager for Millennium Pharmaceuticals, where she managed the company's alliances with Monsanto and Aventis.

Filed under

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.