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This wiki hosts general, public information about the [http://gersteinlab.org Gerstein Lab].  Lab members should consult the [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "private"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]
 
<div style="border: 1px solid black; padding: 10px;">[https://www.gersteinlab.org <big>'''Lab Home Page'''</big>]</div>


== Important Public Items ==
== Important Public Items ==
(not on the homepage yet, but will be soon)
*Gerstein Lab '''[https://www.youtube.com/channel/UCVM3Kd2UWdJrAfQ1RqyajHw Youtube]''' , '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''
*'''[[FAQ]]''' on tools and data
*'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''
*[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]])
*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab
*[[Summaries]] of lab research (with shadow internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet])


*Public [[Documents]] about the lab
== Key Info for Lab People (esp. new ones) ==
===Software and tools===
* Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.
*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
* Initialed people should have access to a [https://bit.ly/mglab-general Google Drive] (or quickly via [https://bit.ly/mglab-general '''bit.ly/mglab-general'''])
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
* [[Glossary]] of terms.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
* Pointers on [[Draft Flow]] (Ideas related to the process of drafting and submitting papers, which contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ([https://info.gersteinlab.org/index.php?title=Proofsx57m&redirect=no '''Proofsx57m''']))
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
<BR>
<br>
__TOC__
*[[FAQ]] (new) on programs
*Prominent [[public wiki pages linked from elsewhere]]


In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [https://privatewiki.gersteinlab.org/ private lab wiki] for lab-specific information (login as user "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]


==Job opportunities==
<HR>


====Post-doctoral Position in Bioinformatics at Yale====
== Other Stuff for the Public ==
Applicants are invited for a post-doctoral position at [http://www.yale.edu/ Yale University]. The position is for two years with possible extensions. Choice of project would to some degree depend on the applicant's interests and abilities, though it is expected that the research will be purely computational and will fall into a number of sub-areas in the emerging field of bioinformatics. For specifics, see lab research areas [http://www.gersteinlab.org/about here]. Also, see an [http://papers.gersteinlab.org/papers/subject/intro-to-lab/ introduction to the lab] and some of our best [http://papers.gersteinlab.org/papers/subject/best2006/ papers].
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Posters]] showing lab research
*Misc. Public [[Documents]] about the lab
*Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]], [http://linkstream.gersteinlab.org/tag/seminars Just seminars])
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]


The ideal applicant would have a PhD (preferably in bioinformatics, biophysics, or computer science) and have already had some experience in one of the above-mentioned research areas. However, a non-biological background with strong training in another area of science (e.g., physics or computer science) would also be appropriate. He or she would be very skilled in programming and using the computer to solve problems (e.g. experience with C/C++, perl5, SQL, HTML/java, fortran, O/X-PLOR, blast/fasta, excel/word, Irix/linux, and so on).
== Info for Lab Signature ==
*For all lab signatures this the procedure: ask LI & CC. MG will reply w/ an email say "sign0mg" LI will sign.


Further contact information is available [http://www.gersteinlab.org/people/contact.html here]. Applicants are requested to send a CV that includes a list of publications and details of 3 references. Normal e-mail is OK for all correspondence. However, copies of official documents should follow by regular post. Further details about the position and bioinformatics research at [http://www.yale.edu/ Yale] can be obtained over the web at:
== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]
* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.  
** [[Gerstein Lab Computing in HPC]]
** [[Gerstein Lab Computing in GersteinLab West Campus]]
** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]


<center>'''http://www.gersteinlab.org'''</center>
* Calls, meetings, &c
**A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.com GLMinutes.wordpress.com] (more info about the [[Wordpress Minutes Stream]])
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
**  [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&on=downloads Other info])
**[[Bass434]] introduction
**Booking [[Meeting Room]]
**Booking a [[Conference Room at 100 College]]


====Summer Job in Bioinformatics at Yale====
* Some Useful University Policies
A summer job is available during the upcoming summer to assist in scientific research at Yale University. Possible projects include either elaborating the web interface to an existing biological database (http://www.molmovdb.org) or doing a variety of calculations in genomics. It is expected that this job would be purely computational in nature and consequently require very good computer skills. Experience with such things as C/C++, perl5, SQL, linux/Irix, HTML, and cgi/Java is highly desirable. The salary is negotiable depending the degree of committment.
** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]
 
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
Further contact information is available [http://www.gersteinlab.org/people/contact.html here]. Applicants are requested to send a CV that includes a list of publications and details of 3 references. Normal e-mail is OK for all correspondence. However, copies of official documents should follow by regular post. Further details about the position and bioinformatics research at Yale can be obtained over the web at:
** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf  old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]
 
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
<center>'''http://www.gersteinlab.org'''</center>
** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3  Yale Purchasing Buy/Pay Matrix 3401.3]
 
====PhD Studentships in Bioinformatics at Yale====
Students interested in bioinformatics should apply via the Computational Biology and Bioinformatics (CBB) track in the Biological & Biomedical Sciences (BBS) program, being sure to indicate interest in this lab to enable proper routing of the application. More information through [http://www.cbb.yale.edu/ CBB Home Page] and [http://bbs.yale.edu/ BBS Program].
 
====Undergraduate Researcher in Bioinformatics at Yale====
A number of undergraduate research positions are available during the academic year. Depending on the nature of the work and the student's interest, these positions can either be paid (at normal undergraduate rates) or in the framework of research courses, such as MB&B 470 or CPSC490
There is a wide range of projects with both a computational and biological perspective. These range from elaborating the web interface to an existing biological database (e.g. http://www.molmovdb.org, http://pseudogene.org), to doing a variety of calculations on genomes, from processing and analyzing next-generation sequencing data, to building a machinery for network calculations.
 
It is expected that these jobs will be purely computational in nature and consequently require very good computer skills. Experience with such things as C/C++, Perl/CGI, SQL, Linux/Irix, HTML and Java is highly desirable. Knowledge of statistical softwares, such as R, Matlab, ROOT, etc., would also be desirable. The salary is negotiable depending the degree of committment.
 
Please contact Mark Gerstein (Mark.Gerstein at Yale.edu) for further information. Normal e-mail is OK for all correspondence. Further details about the lab and bioinformatics research at Yale can be obtained over the web at:


<center>'''http://www.gersteinlab.org'''</center>
* Documents
** [[Uploading_documents]]
** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates)


== Info for New People ==
* Misc
*[[General Information for New Undergraduates]] thinking about working in the lab
**[[Getting Mark's signature for documents]]
* Information for <B>new people</B> starting in the lab from the private wiki ([http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure], [http://wiki.gersteinlab.org/labinfo/Bad_Times_and_Contact_Info], [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab], [http://wiki.gersteinlab.org/labinfo/Staff])
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
 
**Prominent [[public wiki pages linked from elsewhere]]
== Info for Lab Members and Collaborators ==
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
*[http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
*[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
*[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
** [[Recommendation Letters]]
*[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
*[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
* [[Streamlining Draft Flow]] (Ideas for streamlining the process of drafting and submitting papers)
** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]
** Way to list Mark's [[Affiliation]] on papers
** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
** See [[xxmg at gersteinlab.org | xxmg@gersteinlab.org]] for correct address to use for paper correspondence.
**[[OpenStack]]
** Note that '''xxmg at bioinfo.mbb.yale.edu''' for paper correspondence is deprecated.
**[[IDP report]]
* [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
**[[PEC package preprints]]
* [[Recommendation Letters]]
**[[Summary of undergraduate involvement]]
* Lab [[Resources Document]] (NIH form)
**Lab [http://bit.ly/mglab-folder google folder]
* [[Papers Page Code]]
**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]
* Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
* Some Useful University Policies
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]], [http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf  Policy on Minors in Labs], [[Policy on Postdoc Appointments]]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
* Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]
* [http://maguro.cs.yale.edu:8000/Center_for_High_Performance_Computation_in_Biology_and_Biomedicine Yale High Performance Computing Center]
* Information on [[what grant to charge something to]]
* Information on [[Meeting Invites]]
* [http://araman.mbgnet/nagios/ System Status] MBGNet LAN access only.

Latest revision as of 01:57, 31 May 2026

Important Public Items

Key Info for Lab People (esp. new ones)


In general, this wiki hosts general, public information about the Gerstein Lab, beyond that on the homepage. Lab members should consult the private lab wiki for lab-specific information (login as user "public"). To edit this wiki, contact the Infoadmin

Other Stuff for the Public

Info for Lab Signature

  • For all lab signatures this the procedure: ask LI & CC. MG will reply w/ an email say "sign0mg" LI will sign.

Info for Lab Members and Collaborators

Retrieved from "https://info.gersteinlab.org/index.php?title=Main_Page&oldid=6489"