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Downloads and Upgrades: TranSMART 1.1, Mascot Insight, SoftGenetics Free CNV Analyses, and more

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The TranSMART Foundation has launched a new version of the open source knowledge management platform.

Version 1.1 includes features such as a new application programming interface layer that removes direct dependency on the I2B2 API, and I2B2 server, while preserving the underlying database and functionality, and improvements to the ETL process among other updates.


Matrix Science, protein identification software developer, has launched Mascot Insight, a new software application for organizing, visualizing, and comparing proteomics data derived from mass spectrometry.

It includes tools for annotating results individually or as a group, providing them as tabulated or graphical reports, and exporting them in machine-readable formats. It includes a data exploration tool that lets users organize results in folder, merge results, as well as capabilities for filtering reports using criteria such as Gene Ontology, GO, classifications among other features.


This week, Genomatix added a new application to BaseSpace Apps, Illumina's informatics application store.

The new app, Genomatix Pathway System, lets users generate and visualize genetic networks and pathways. It also provides information on genes, gene-gene connections as well as gene expression data.


SoftGenetics said this week that it will offer up to 10 free copy number variation analyses using its NextGene software to interested next generation sequencing users.

To take advantage of this offer, interested researchers need to electronically provide up to 10 individual whole exome samples or targeted panels BAM files as well as one control BAM file. Furnished BAM files must be sanitized of identifying information.


DNAStar has released Lasergene 11.2.

This version of the sequence analysis software incorporates new alignment methods and tools in the MegAlign Pro application. It also supports Clustal Omega, Mauve, a Muscle alignment algorithm, and enhanced phylogenetic trees.


BioData has launched a free mobile app for Labguru, its web-based research and lab management software.

The app is available for both iPhone and Android phones. It lets researchers photograph, annotate, catalog, and share experimental results, whiteboard drawings, conference posters, or visual notes for performing a step of an experiment. The app can also be used to find samples, reagents, as well as supplies’ locations and expiration dates on the go.

BioData also announced this week that later this year, it will a new feature to the web-based version of Labguru called UpFolder that will automatically sync data files from instruments to the cloud and the appropriate experimental records housed inside Labguru. It will also update the mobile version of Labguru so that users will be able to request supply orders and be notified when the supply arrives. Future releases of the app will also include tools for running and timing multiple experiments at the bench as well as recording experimental results.


Core Informatics has released a new version of its integrated product suite, a system, which provides customers with all the tools they need to manage data in their laboratories.

Version 4.2 of the suite includes dashboard displays with administrator-defined dynamic content so organizations can share reports in real time as well as the ability to create schedules for any objects allowing scientists to reserve, monitor, and trend objects like laboratory instruments, testing facilities, and critical reagents. Furthermore, administrators now have the ability to define transfer maps for non-standard transfers and expanded trigger capabilities for automating data capture using CoreScript, a new engine for automating unique laboratory workflows.


RefSeq 61 is now available through the National Center for Biotechnology Information via ftp.

The release includes 41,958,567 records, 33,139,114 proteins, 4,528,216 RNAs, and sequences from 29,414 different organisms.


The genome browser group at the University of California, Santa Cruz has released a new set of public custom tracks for zebrafish and tetraodon.

These tracks include CAGE transcription start site information for multiple developmental stages for both genomes, plus H3K4me3 methylation and RNAseq data for zebrafish.


Linguamatics has released I2E version 4.1.

The newest version of its text-mining platform offers more streamlined access to content by linking enterprise servers with content servers in the cloud. It also offers enhanced chemical querying capabilities including substructure and similarity searching, and it integrates chemical structure drawing using chemistry components from ChemAxon.


The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.