Main Page

From GersteinInfo

(Difference between revisions)
Jump to: navigation, search
(Undergraduate Researcher in Bioinformatics at Yale)
(Info for Lab Members and Collaborators)
 
(204 intermediate revisions not shown)
Line 1: Line 1:
-
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]]
 
-
 
== Important Public Items ==
== Important Public Items ==
-
(not on the homepage yet, but will be soon)
+
*Gerstein Lab '''[https://twitter.com/GersteinLab Twitter]'''
 +
*'''[[FAQ]]''' on tools and data
 +
*'''Lab [[Calendar]]'''
 +
*[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
 +
*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab
 +
-
*Public [[Documents]] about the lab
+
__TOC__
-
===Software and tools===
+
-
*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
+
-
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
+
-
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
+
-
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
+
-
<br>
+
-
*[[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 [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 "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)
 +
*[[Summaries]] of lab research
 +
*[[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 New People ==
 +
* Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.
-
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 [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
 +
*** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist]
 +
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
 +
** [[CRAMTOOLS and common directory]]
-
<center>'''http://www.gersteinlab.org'''</center>
+
* 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]
-
====Summer Job in Bioinformatics at Yale====
+
* Calls, meetings, &c
-
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.
+
**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])
 +
** [[Zoomrooms]] in BASS 434
 +
**[[Whiteboard camera system]] in BASS 434
 +
**[[IR remote-Logitech Harmony express]] in BASS 434
 +
**Booking [[Meeting Room]]
-
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:
+
* Some Useful University Policies
 +
** [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]]
 +
** 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]
 +
** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3  Yale Purchasing Buy/Pay Matrix 3401.3]
-
<center>'''http://www.gersteinlab.org'''</center>
+
* Documents
 +
** [[Uploading_documents]]
 +
** Letterhead templates (at http://wiki.gersteinlab.org/labinfo/index.php/Templates)
-
====PhD Studentships in Bioinformatics at Yale====
+
* Misc
-
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].
+
**[[Getting Mark's signature for documents]]
-
 
+
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
-
====Undergraduate Researcher in Bioinformatics at Yale====
+
**Prominent [[public wiki pages linked from elsewhere]]
-
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
+
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
-
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.
+
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
-
 
+
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
-
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.
+
** [[Recommendation Letters]]
-
 
+
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
-
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:
+
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
-
 
+
** 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]
-
<center>'''http://www.gersteinlab.org'''</center>
+
** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
-
 
+
**[[OpenStack]]
-
== Info for New People ==
+
**[[IDP report]]
-
*[[General Information for New Undergraduates]] thinking about working in the lab
+
**[[PEC package preprints]]
-
* 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])
+
**[[Summary of undergraduate involvement]]
-
 
+
**Lab [http://bit.ly/mglab-folder google folder]
-
== Info for Lab Members and Collaborators ==
+
**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]
-
*[http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
+
-
*[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
+
-
*[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
+
-
*[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
+
-
*[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
+
-
* [[Streamlining Draft Flow]] (Ideas for streamlining the process of drafting and submitting papers)
+
-
** Way to list Mark's [[Affiliation]] on papers
+
-
** See [[xxmg at gersteinlab.org | xxmg@gersteinlab.org]] for correct address to use for paper correspondence.
+
-
** Note that '''xxmg at bioinfo.mbb.yale.edu''' for paper correspondence is deprecated.
+
-
* [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
+
-
* [[Recommendation Letters]]
+
-
* Lab [[Resources Document]] (NIH form)
+
-
* [[Papers Page Code]]
+
-
* 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 14:46, 16 May 2022

Important Public Items


Contents


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"). There's also a wiki for lab meetings (login as user "public"). To edit this wiki, contact the Infoadmin


Other Stuff for the Public

Info for New People

  • Please follow the steps of Onboarding to apply and fill in the new members’ entry process.

Info for Lab Members and Collaborators

Personal tools