Dear HMS Research Software Users,
Our August 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.
GenomePilot Evaluation
A number of you attended the GenomePilot Workshop that we hosted on August 10th. In conjunction with this workshop HMS has access to a license to evaluate the software through September 6th. Please be sure to try out GenomePilot and let us know your thoughts. If you need an account to access the software, please email us at help@biogrids.org.
Software Training
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees: HMS's Research Computing group: no new courses posted.
The Countway Library has space available in their SHRINE workshop: How to use the SHRINE web-based tool to generate an aggregate number of patients across Harvard hospitals.
The Harvard Chan Bioinformatics Core: has announced several upcoming workshops including a 2-day Introduction to R workshop Sept 29-30, an Introduction to Differential Gene Expression analysis workshop on October 20th, and an 8-day in-depth course on NGS Data Analysis using RNA_Seq.
The SBGrid Consortium will host a PyMOL webinar on September 13th featuring Schrödinger Senior Applications Scientist Daniel Cappel.
Software Installation
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'.
**New Software:
Updated Software:
- Anaconda has jumped from version 2.4.1 to 4.1.1] in an effort to avoid confusion with the versions of Python included in Anaconda. The highlights of this release include a new Navigator GUI for managing conda environments and applications and the addition of Jupyter Notebook Extensions.
- CCP4 version 7.0.18, includes many updates and changes, a full listing of which you can find on their Updates Page.
- Ghostscript version 9.19 is the new default. This software has had a number of releases since our last update and a full listing of changes can be found in their release notes.
- EMAN2 version 20160805 includes a new Tophat filter in e2refine_easy.py: --tophat. This option was added to satisfy the call for a 'sharper' map, despite Ludtke's mixed feelings about the appropriateness of the filter.
- pandas version 0.18.1 s a minor release that includes an enhancement to .groupby(...) to provide convenient syntax when working with .rolling(..), .expanding(..) and .resample(..) per group, an option to assemble dates from a DataFrame using pd.to_datetime(), and method chaining improvements, along with the usual bug fixes.
- Spider version 23.03 is the new default for Linux. This update includes several new operations, including DOC SLICE to put a slice from one document file into a new document file, DIS to convert SPIDER image to JPEG , RI R and RI RV to examine positions of rings in power spectra or CTF images, CP TO STK to merge a series of stacks into a single new stack, and FSC NEW to find FSC and resolution. You'll also find that the Three Dimensional Reconstruction protocol for single particle reconstruction now incorporates a 'gold standard resolution' workflow.
- MACS2 version 2.1.1 has a number of new features. Callpeak has a more flexible format, users can define the left and right position of the ChIPed fragment, MACS2 will skip model building and directly pileup the fragments, and the 'tempdir' can be specified. New operations were also added to, to calculate the maximum and minimum values in BEDGRAPH against another BDGRAPH file or a given value (bdgcmp and bdgopt).
Feedback Please
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 help@biogrids.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:
fasta
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 help@biogrids.org.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.