Dear HMS Research Software Users,
Our July 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.
Software Training Update
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees: HMS's Research Computing group: no new courses listed.
The Countway Library is offering a SHRINE workshop: How to use the SHRINE web-based tool to generate aggregate number of patients across Harvard hospitals. Registration is ongoing.
The Harvard Chan Bioinformatics Core has announced new workshops for the fall including, a 2-day Introduction to R workshop, a 1-day workshop on Differential Gene Expression analysis, and an 8-day in-depth NGS data analysis course. Registration for these courses has not yet started, but the classes usually fill quickly, so mark your calendars. Users can submit applications for the NGS course beginning August 25th.
The SBGrid Consortium will host a PyMOL webinar on September 13th featuring Schrödinger Senior Applications Scientist Daniel Cappel.
BioGrids is hosting a GenomePilot Workshop on Wednesday, August 10th from 1:30-4:30pm in SGM106. Attendees will have free access to the GenomePilot server for four weeks following the workshop.
Register here http://goo.gl/forms/h9ecFrdSjwlCVQ983 to save your space. The workshop is free, but PIs will be charged $100 for no-shows. Please note that only a few open spaces remain, but if we have broad interest, we may be able to schedule additional sessions.
GenomePilot bridges the gap between bioinformatics and the Next Gen Sequencing lab to simplify the analysis of NGS data. In this workshop you will learn how to create and run a process for analyzing NGS data using Appistry’s GenomePilot. The workshop will include a demonstration of GenomePilot, an interactive hands-on user experience, and a discussion of applications and issues related to the analysis of NGS data in both a research and clinical setting.
1:30 to 2:30pm – Introduction to GenomePilot for the secondary analysis of NGS data.
2:30 to 3:30pm – Hands-on workshop. Creating and running NGS data analysis pipelines.
3:30 to 4:30 pm – Discussion of topics of interest. Loading of user’s datasets for the GenomePilot evaluation.
SBGrid just posted a new webinar on their SBGridTV YouTube Channel featuring the molecular biology suite, Geneious with Christian Olsen presenting. The webinar gives a general overview and covers sveral topics including Custom BLAST, workflow builder, annotation tools, and CRISPER tools.
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'.
- CCP4 version 7.0.015 introduces a new modularized version of AMPLE, a new glycan viewer in ccp4mg, reworked stereochemistry detection in privateer, and a number of other improvements.
- Picard version 2.5.0 includes an optional MarkDuplicates flag along with several other bug fixes and performance improvements.
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 firstname.lastname@example.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:
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 email@example.com.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.