December 2019 Newsletter
Our December newsletter includes sixty new R packages for version 3.5.1 and two new software titles. We also now make available R version 3.5.1 for Jupyter notebooks across all BioGrids supported platforms. Spring workshop schedules for the Harvard Longwood campus have not been announced yet.
Please be sure to read our note on Max OSX 10.15 below.
BioGrids is not compatible with MacOS 10.15
BioGrids is not compatible with MacOS 10.15 Catalina. Apple enforces strict filesystem controls that will break existing BioGrids installations.
While we recommend not upgrading to 10.15 on any Mac with BioGrids already installed,
we have also implemented a workaround to install BioGrids and SBGrid on new machines.
Apple has also dropped support for 32-bit binaries. We are compiling a list of 32-bit software applications that will not be available in MacOS 10.15.
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.
BioGrids is available to all Harvard affiliates on a trial basis for the 2019 calendar year.
Register here to try out our software installer, which allows users to choose from over 200 bioinfomatics 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 Installer
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 using the link button above and register here for activation.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide over 200 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 
BioGrids QuickStart
If you are new to BioGrids and would like to quickly get started with the command line version, follow the instructions below:
1: Download the BioGrids Installer command line version
Linux CLI
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz
tar zxf biogrids-1.0.694-Linux.tgz
cd biogrids-1.0.694-Linux
OSX CLI
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz
tar zxf biogrids-1.0.694-Darwin.tgz
cd biogrids-1.0.694-Darwin
2: Activate biogrids
./biogrids activate biogrid-production jvinent1 70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==
Replace the site name, user name and activation key with your own credentials.
3: Install software with BioGrids
./biogrids install fastqc trimmomatic samtools star subread igv
When finished, verify applications are installed:
./biogrids installed
Software Updates
R for Jupyter Notebooks
Jupyter is a language-agnostic HTML notebook application for Project Jupyter. BioGrids now provides support for the R programming language within Jupyter Notebooks.
R version: 3.5.1
PRSice2
A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores.
Version: 2.2.11
ImageJ is a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.
Versions: 1.52a
New packages in R version 3.5.1
| classInt |
coda |
| CODEX |
CODEX2 |
| deldir |
DEXSeq |
| diffusionMap |
doRNG |
| dqrng |
e1071 |
| expm |
farver |
| FNN |
furrr |
| gmodels |
googleVis |
| gower |
grImport |
| hwriter |
ipred |
| IRdisplay |
IRkernel |
| lava |
LearnBayes |
| leidenbase |
manipulateWidget |
| miniUI |
misc3d |
| ModelMetrics |
numDeriv |
| pbdZMQ |
pbmcapply |
| pcaPP |
pkgmaker |
| prodlim |
pscl |
| randomForest |
RcppAnnoy |
| RcppParallel |
recipes |
| registry |
repr |
| RhpcBLASctl |
rngtools |
| ROpenCVLite |
rrcov |
| rsample |
RSpectra |
| SC3 |
scatterplot3d |
| scmap |
sitmo |
| slam |
sp |
| spData |
speedglm |
| SQUAREM |
statmod |
| timeDate |
udunits2 |
| units |
uuid |
| uwot |
webshot |
| caret |
WriteXLS |
| BSgenome.Hsapiens.UCSC.hg19 |
|
| WES.1KG.WUGSC |
|
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Spring schedule coming soon.
The Harvard Chan Bioinformatics Core
Spring schedule coming soon.
Countway Library of Medicine
Spring schedule coming soon.
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
BioGirds is supported by Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SGBGrid.
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