Dear HMS Research Software Users,
Our March newsletter includes a listing of scheduled research computing courses at HMS, information on webinars that might be of interest, and updates to our software installation on Orchestra and available for OSX. For additional information about the BioGrids project please visit our HMS website at BioGrids.org.
Software Training Update
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees:
HMS's Research Computing group has a new round of courses offered on topics from Introductory R, Next-Gen Sequnecing, HPC/Orchestra, MATLAB, and Perl/Bioperl to Intermediate Linux/Orchestra. Some courses are already filled, so be sure to register or join the waitlist soon.
The Countway Library has a number of offerings posted, many of which have only a waitlist option, but spaces are still available for:
MetaCore: Getting the most from your "omics" analysis
mRNA-Seq analysis using JMP Genomics software The Harvard Chan Bioinformatics Core has posted two new courses for which registration will open soon: A 2-day Intro to UNIX and RNA-Seq data analysis workshop in May An in-depth NGS data analysis course starting in June being held 2 days per week for 5 weeks. The SBGrid Consortium's Advanced Crystallography course is sold out. This course will focus on indexing, integration, and scaling of challenging datasets and initial model building.
CRANK2 was the focus of the recent SBGrid Consortium webinar series. If you're interested in this structure solution software, you can watch the webinar on the SBGrid YouTube channel.
SBGrid will host another webinar on April 26th, focusing on AMPLE: a pipeline for unconventional Molecular Replacement. Tune in then or subscribe to the SBGrid channel for updates. Webinar details are posted on the SBGrid website.
New titles and software updates were pushed out to the BioGrids software collection. 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'.
- ABySS version 1.9.0 is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
- BCFtools was added to BioGrids collection for Linux last month, and is now available for Mac OSX.
- Bowtie2 version 2.2.8 was pushed out and included some minor fixes.
- breseq was updated to version 0.27.1
- Cufflinks version 2.2.1, previously available for Linux only, is now available for Mac OSX.
- cython version 0.23.4, installed as a Python module, is a major update. New features include PEP 492 (async/await) and PEP 448 (star-unpacking generalizations), inlined generator expressions, added support for the C++ assignment and bool() operators and for coverage analysis.
- DIAMOND version 0.7.11 is primarily a bug fix release.
- Fastqc version 0.11.5 added support for processing files of Oxford Nanopore reads and fixes a number of bugs.
- HISAT2 was added to the BioGrids collection for Linux last month, and is now available for Mac OSX.
- IGV version 2.3.68 is the new default. Since the last update we pushed, a number of new features have been added including new options to do a BLAT search from a feature, alignment, or region of interest, to combine numeric tracks, to add gene lists in "bed" format, and to hide alignments when loading BAM files, showing coverage and/or splice junctions only.
- MAFFT version 7.273 has improved parallelization efficiency when the number of sequences is large and sequence length is short.
- MODELLER version 9.16 is primarily a bugfix release.
proDy version 1.7, installed as a Python module. proDy is a protein structural dynamics analysis software package.
pysam version 0.8.4, also installed as a Python module. pysam makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages.
We'd like to hear from you! Please remember that we can only improve the collection with feedback from the community. If you would like to see a title added to BioGrids on Orchestra or OSX, please send details to firstname.lastname@example.org or submit a support request on the BioGrids.org website. You can also communicate your request through the HMS IT Research Computing group, or our RC liaison Kristina Holton.
Instructions for Orchestra Users
Getting started with BioGrids: if you have already configured your environment, you will see "Software Supported by BioGrids" in your login shell message. If you don't see this message: - run the command /programs/biogrids_setup - This script allows the user to run BioGrids and asks if you wish to modify your startup files. If yes, the setup script will add this line to your environment: 'source /programs/biogrids.shrc'. You can remove this line and recover your old environment at any time. If no, only your current shell will be configured to access the BioGrids collection. To configure BioGrids in the future, you can use these lines as an alternative to running biogrids_setup: bash: source /programs/biogrids.shrc or tcsh: source /programs/biogrids.cshrc - Once your environment is configured, you can launch applications from your shell or script without any additional settings, e.g. to run fasta, enter fasta on the command line:
To see the full list of installed applications cat '/programs/x86_64-linux/biogrids_x86_64-linux'.
If you have any problems activating this setup, please email email@example.com.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.