Monthly Archives: March 2017

Highlights of 2016

I recently had to complete my 2016 Faculty Activity Report (FAR), summarizing key lab “activities” of the past year.

* Here are dump directories with some excerpts:

http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary–cv57/ http://files.gersteinlab.org/public-docs/2017/03.26/2016-summary–cv57/

These include:

* A full updated CV describing my lab’s activities (in too much detail):

http://files.gersteinlab.org/public-docs/2017/03.26/2016-summary–cv57/M-Gerstein-Public-CV–bld1dec16.cv57.pdf

The CV is based on :

– Compiling the people in the lab, viz:

http://files.gersteinlab.org/public-docs/2017/03.26/2016-summary–cv57/cv57-22-bld1dec16-AdaptedFrom–Gerstein_Lab_Personnel_112016.pdf

http://files.gersteinlab.org/public-docs/2017/03.26/2016-summary–cv57/cv57-23-bld1dec16–EditOn–Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf

– A dump up to the end of ’16 of all of our scientific papers and our “other writings” too.

http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary–cv57/cv57-26-bld1dec16–addendum-Rest–Just-Other-Writings.pdf

http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary–cv57/cv57-30-bld1dec16–papers-simple–reformatted.pdf

– There’s also an update on lectures in ’16:
http://lectures.gersteinlab.org/summary/

* Finally, I’ve done little write up of some highlights, viz:

During 2016 the lab had a number of research highlights. We have published three interlinked tools: Stress, Frustration, and
Intensification, for assessing the impact of rare genomic variants using knowledge of molecular structure. The tools are of particular interest to the medical genetics community because as they can help explain various cancer mutations as well as variants associated with genetic diseases. Another highlight is our publishing a framework for quantifying privacy risks as a result of linking clinical and phenotype variables. This paper is a timely work given the ongoing debate on data sharing. Apart from these works, we have a few research papers on topics in genomics, such as analyzing allele-specific binding and gene expression analysis, and several review articles on the role of non-coding variants, network comparison, and the cost of sequencing.

Regarding service, I worked on further developing the computational biology program at Yale. In particular, I co-chaired a committee about moving toward a Center for Biomedical Data Science at the Medical School. My lab served the research community in participating in many consortiums, such as PCAWG (the Pan-Cancer Analysis Working Group), the ENCODE consortium, PsychENCODE, 1000 Genomes’ structural variation group (and its follow-ons), and the Extracellular RNA Communication Consortium. In 2016, I gave talks and participated in many meetings, including an important data-science education forum at the Cold Spring Harbor Laboratory.

Regarding teaching, I further developed my course in Bioinformatics by including more practical hands-on materials. For example, we introduced a collaborative programming assignment utilizing the GitHub site.

(Private link, with authentication only for my reference:
http://facultyadmin.yale.edu/far/mark-gerstein)

For reference, this involved updating a variety of places on the wiki, viz:

http://info.gersteinlab.org/MBG-Profile
http://info.gersteinlab.org/Additional_Information_about_Personnel http://info.gersteinlab.org/Pubmed_query#Misc

Genes, environment, and “bad luck” | Science

Quite relevant….
==

Genes, environment & bad luck
http://science.ScienceMag.org/content/355/6331/1266 To what degree are #cancer mutations due to replication error (3rd factor), not 1st 2?

discusses R v D correlation

Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention Cristian Tomasetti1,2,*, Lu Li2, Bert Vogelstein3,*
Science 24 Mar 2017:
Vol. 355, Issue 6331, pp. 1330-1334
DOI: 10.1126/science.aaf9011
http://science.sciencemag.org/content/355/6331/1330

Farnam partition

The absolute path is "/ysm-gpfs/pi/gerstein/". Please put most of your data here.

After creating the folder (don’t forget to set up chmod the way you like), then you can create a soft link your folder back to your home folder for quick access.

ln -s [your folder under pi] [the soft link under your home folder (aka ~/xx )]

Instructions on setting up ssh desktop clients for Farnam

1) It is possible to set up ssh such that you only have to authenticate once; subsequent ssh’s reuse that connection. Please see our detailed instructions here:

http://research.computing.yale.edu/support/hpc/user-guide/ssh-sample-configuration

2) We have detailed instructions on how to use Cyberduck and Winscp to connect using duo on our website. Please see:
http://research.computing.yale.edu/support/hpc/user-guide/transfer-files-or-cluster

I believe it is also possible to use filezilla after doing a similar configuration to avoid the creation of new connections, but don’t see the need, given that cyberduck and winscp are both usable.

Farnam dedicated queue

There is a hard limit on the number of cores available per user at Farnam general queue (QOSMaxCpuPerUserLimit). As an alternative, the gerstein group has a large dedicated partition (pi_gerstein) which has no per user limit.

Use the parameter –partition pi_gerstein or -p pi_gerstein when submiting jobs to Farnam’s slurm.

Farnam dedicated queue

There is a hard limit on the number of cores available per user at Farnam general queue (QOSMaxCpuPerUserLimit). As an alternative, the gerstein group has a large dedicated partition (pi_gerstein) which has no per user limit.

Use the parameter –partition pi_gerstein or -p pi_gerstein when submiting jobs to Farnam’s slurm.

[tag: farnam, cpu, slurm, queue]