Dear HMS Research Software Users,
Our November newsletter includes information on updates to our Orchestra software installation, Mac OS X software support, a beta version of our workstation software installer, and a listing of scheduled research computing courses at HMS. For additional information about the BioGrids project please visit our HMS website at BioGrids.org.
BioGrids on your Mac
The new beta Workstation Installer for BioGrids, which installs the BioGrids collection on your laptop, is available to quad-based HMS labs. Software titles are added and updated regularly and a complete list of supported applications can be found on BioGrids.org. The installer allows the user to select the desired applications and, once installed, applications are accessed as they are on Orchestra To get started complete this Google Form and be sure to email us at firstname.lastname@example.org if you encounter any problems or have questions.
Software Training Update
We would like to highlight a few bioinformatics training sessions that will be offered to HMS trainees:
- The Countway Library is still accepting registrations for classes that will be held in December and January, including: Affymetrix and Illumina microarray data analysis using R/Bioconductor, Analyzing Next generation sequencing Data: Standard data processing and workflow analysis, mRNA-Seq analysis using JMP Genomics software, and Introduction to ChIP‐Seq and data analysis using Galaxy
- The Harvard Chan Bioinformatics Core is now accepting applications for an in-depth course on NGS-based genomic analysis that comprises 5 hands-on sessions over a 5-week period beginning in February. The application deadline is November 25th.
October Software Updates
3 new titles were added to the BioGrids software collection, for a total of 83, along with 4 updates. For a full listing of installed applications, see the BioGrids.org website or for Linux: cat the file '/programs/x86_64-linux/biogrids_x86_64-linux'.
Software - New
- Bioconductor version 3.1 Package EBSeq version 1.10.0, an R package for gene and isoform differential expression analysis of RNA-seq data, was added for R version 3.2.2.
- Cytoscape version 3.2.1 (Mac only) is a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
- RSEM version 1.2.25 (Linux only) is (RNA-Seq by Expectation-Maximization) for estimating gene and isoform expression levels from RNA-Seq data.
Software - Update