September 2022 Newsletter
Our September newsletter includes seven new and updated titles for Mac and Linux. New software titles can be requested by sending email to help@biogrids.org or filling out our webform:
https://biogrids.org/help/?tab=software
Remote Working Help
The BioGrids Wiki provides step by step instructions for installing BioGrids software on a local laptop or desktop machine. If you prefer a live demonstration, or run into trouble, please contact help@biogrids.org. We can set up a Zoom meeting to assist you.
MacOS 10.15 Catalina
Due to new security measures in OSX, installation under MacOS 10.15 requires an additional step. We have detailed a workaround to install BioGrids and SBGrid on new machines. Two approaches are available.
Cite BioGrids
If your use of BioGrids supplied software was an important element in your publication, please include the following statement in your work:
"Software used in the project was installed and configured by BioGrids
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
See our Grant Support page for additional details.
Register here to try out our software installer, which allows users to choose from over 530 bioinfomatics and life sciences tools that can be installed as ready-to-run applications on Mac or Linux machines with the click of a button or a short command from the CLI. No need to worry about dependencies or compilation.
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members. This includes all aspects of software installation and management. If you need assistance of any kind please send a note to: help@biogrids.org.
BioGrids Quickstart
The latest version of the BioGrids Installation Manager is available for Linux and MacOS computers:
macOS: Installation Manager 2.6.17
Linux: Installation Manager 2.6.17
Start the BioGrids environment:
source /programs/biogrids.shrc
List available titles (Linux):
cat /programs/x86_64-linux/biogrids_x86_64-linux
List available titles (Mac):
cat /programs/i386-mac/biogrids_i386-mac
Get version and override info:
biogrids-info -l star
Get list of executables for a title:
biogrids-list star
Need more help? Send mail to: help@biogrids.org
Software Updates
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:1.16 | Linux 64 1.16 | OS X INTEL
SeqKit is a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.
Updated versions:2.3.1 | Linux 64 2.3.1 | OS X INTEL
smoove is a structural variant calling and genotyping with existing tools, but, smoothly.
Updated versions:0.2.8 | Linux 64
SAMtools (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:1.16.1 | Linux 64 1.16.1 | OS X INTEL
poretools a toolkit for working with nanopore sequencing data from Oxford Nanopore
Updated versions:0.6.1a1 | Linux 64 0.6.1a1 | OS X INTEL
MDAnalysis an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
Updated versions:2.2.0 | Linux 64 2.1.0 | Linux 64 2.2.0 | OS X INTEL 2.1.0 | OS X INTEL
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
Updated versions:7.3.2 | OS X INTEL 7.3.2 | Linux 64
Software Training
Center for Computational Biomedicine
The Center for Computational Biomedicine (CCB) Fall newsletter contains training and collaboration opportunities.
HMS Research Computing
User Training Fall 2022 registration is now open.
| Class |
Date |
Time |
| Intro to O2 |
9/7/2022 |
10am-12pm |
| |
9/14/2022 |
no class |
| Intro to O2 Portal (new workshop) |
9/21/2022 |
10am-12pm |
| Optimizing O2 Jobs |
9/28/2022 |
10am-11am |
| Intro to MATLAB |
10/5/2022 |
10am-12pm |
| Intro to Parallel Computing |
10/12/2022 |
10am-12pm |
| Intro to Python |
10/19/2022 |
10am-12pm |
| Intermediate O2 |
10/26/2022 |
10am-12pm |
| Intro to Git/GitHub |
11/2/2022 |
10am-11am |
| RCBio: Easy and Quick HPC Pipeline Builder and Runner |
11/2/2022 |
11am-12pm |
| Intro to Python |
11/9/2022 |
10am-12pm |
| Intro to O2 |
11/16/2022 |
10am-12pm |
| |
11/23/2022 |
no class |
| Intro to O2 Portal (new workshop) |
11/30/2022 |
10am-12pm |
Bioinformatics Support
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: help@biogrids.org
BioGrids is supported by Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SBGrid.
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