November 2021 Newsletter
Our November newsletter includes eight new and updated software titles, including three new versions of GPU based Tensorflow.
As a reminder, new software titles can be requested by sending email to help@biogrids.org or filling out our webform:
https://biogrids.org/help/?tab=software
End Of Life for Version 1 BioGrids Installer
BioGrids installation managers in the 1.X series will no longer work. The last released version was 1.0.695. Attempting installation with this older version will fail and will appear to be a network connection issue. Please upgrade to the new installation manager.
You do not need to reinstall titles or reactivate. Simply download the new Installation Manager and begin using.
Download MacOS and Linux versions from our wiki downloads page:
https://biogrids.org/wiki/downloads.md
We welcome any and all feedback from the community at help@biogrids.org.
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 2.5.12
Linux: Installation Manager 2.5.12
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
TensorFlow Federated (TFF) is an open-source framework for machine learning and other computations on decentralized data.
Versions: 0.19.0 | Linux 64
AlphaPept a modern and open framework for MS-based proteomics.
Versions: 0.3.29_cu11.0.3 | Linux 64
cellxgene an interactive explorer for single-cell transcriptomics data
Versions: 1.0.0 | Linux 64
Transformers State-of-the-art Natural Language Processing for Jax, Pytorch and TensorFlow.
Versions: 4.12.3 | OS X INTEL 4.12.3_cu11.0.3 | Linux 64
TensorFlow an open source software library for high performance numerical computation.
Versions: 2.6.0_cu11.2.2 | Linux 64 2.5.0_cu11.2.2 | Linux 64 2.4.0_cu11.0.3 | Linux 64
QTLtools is a tool set for molecular QTL discovery and analysis.
Versions: 1.3.1 | Linux 64
Python a general-purpose, interpreted, object oriented, high-level dynamic programming language.
Versions: 3.8.8 | Linux 64
Horovod Distributed training framework for TensorFlow, Keras, PyTorch, and Apache MXNet.
Versions: 0.23.0 | Linux 64
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Please see the HMS Research Computing Training Portal for the most current updates.
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Class
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Date
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Time
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Intro to R/Bioconductor
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Dec. 1, 2021
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3-5pm
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Introduction to Globus Data
Transfer and Data Collaboration
on O2
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Dec. 8, 2021
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3-5pm
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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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