November 2018 Newsletter
Our November update brings 8 new software titles and 3 updates, 5 new workshops and classes available on the Harvard Longwood campus, a reminder to connect with us during our weekly BioGrids office hours, and details on how to download BioGrids Software Installer and get started today.
BioGrids Office Hours
BioGrids office hours are held on Wednesdays from 9:00am - 10:00am via Zoom meeting. Want to see what BioGrids is and how it works? Join us for a quick demo. If you prefer to meet in person feel free to stop in 202 LHRRB.
Zoom Meeting URL: https://zoom.us/j/653421485 Wednesdays, 9:00 AM Eastern Time
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members that includes all aspects of software installation and management.
This month we include 8 new and 3 updated applications. New applications are marked with an asterisk in the list below for easy scanning.
AmberTools is a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself. Versions: 18 | Linux 64 18 | OS X INTEL
BreakDancer is a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. Versions: 1.4.5 | Linux 64 1.4.5 | OS X INTEL
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. Versions: 1.2.11 | OS X INTEL 1.2.11 | Linux 64
GangSTR is a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over existing tools (e.g. lobSTR or hipSTR) is that it can handle repeats that are longer than the read length. Versions: 1.4 | OS X INTEL 1.4 | Linux 64
HipSTR was specifically developed to deal with short tandem repeats (STRs) in genomic sequences in the hopes of obtaining more robust STR genotypes. Versions: 0.6.2 | OS X INTEL 0.6.2 | Linux 64
HTSlib is a C library for reading/writing high-throughput sequencing data. Versions: 1.9 | OS X INTEL 1.9 | Linux 64
OpenMPI is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Versions: 1.10.7 | Linux 64
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. Versions: 0.2.5b9 | OS X INTEL 0.2.5b9 | Linux 64
PyCap is an interface to the REDCap Application Programming Interface (API). PyCap is designed to be a minimal interface exposing all required and optional API parameters. My hope is that it makes simple things easy & hard things possible. Versions: 1.0 | OS X INTEL 1.0 | Linux 64
SCRAMBle runs as a two-step process. First cluster_identifier is used to generate soft-clipped read cluster consensus sequences. Second, SCRAMBle-MEIs.R analyzes the cluster file for likely Mobile Element Insertions. Versions: 20181105 | OS X INTEL 20181105 | Linux 64
SPAdes (St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets. Versions: 3.13.0 | OS X INTEL 3.13.0 | Linux 64
The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
A command line version is also available for Macs and Linux. Download and activate using the link button below.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide 160 titles in five categories and an additional 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids
Training sessions available to HMS trainees:
Countway Practical Presentation Skills Wednesday, December 5, 2018 11:00am - 1:00pm
Data Skills: Planning for Research Success Tuesday, December 11, 2018 1:00pm - 2:00pm
Countway Practical Presentation Skills Wednesday, December 19, 2018 5:00pm - 6:30pm
Intro to Git/Github Wednesday, December 5, 2018 3:00pm - 5:00pm
Intro to O2 Wednesday, December 19, 2018 3:00pm - 5:00pm
Need help getting software installed on new machines? Have you been planning to try Amazon Web Services (AWS) cloud computing?
BioGrids can help you get started. We have expertise in bioinformatics, programming, workflow development and high performance computing.
We improve the collection with feedback from the community.
Want to see a new application in BioGrids?
Let us know: firstname.lastname@example.org
BioGrids is supported by the HMS TnT fund and based upon SBGrid.org