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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]]
 
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== Important Public Items ==
== Important Public Items ==
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(not on the homepage yet, but will be soon)
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*[[Selected Press Accounts Highlighting Gerstein Lab Work| '''Press Accounts''']] highlighting the lab
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*'''[[FAQ]]''' on tools and data
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*'''Lab [[Calendar]]'''
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*[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 )
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*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab
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*Public [[Documents]] about the lab
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__TOC__
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===Software and tools===
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*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
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*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
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*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
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*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
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<br>
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*[[FAQ]] (new) on programs
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*Prominent [[public wiki pages linked from elsewhere]]
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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]]
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==Job opportunities==
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<HR>
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====Post-doctoral Position in Bioinformatics at Yale====
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== Other Stuff for the Public ==
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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].
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*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
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*[[Summaries]] of lab research
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*[[Posters]] showing lab research
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*Misc. Public [[Documents]] about the lab
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*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])
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*[[Status of Lab Web Resources]]
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*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]
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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).
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== More Info for New People ==
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* [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab Information] for <B>new people</B> starting in the lab from the private wiki
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* [http://wiki.gersteinlab.org/labinfo/Staff People] to look for to get oriented
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* About [http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure Group Meetings and JClubs]
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*[[Documentation on Shared Google Folder & Dropbox Folder]]
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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:
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== Info for Lab Members and Collaborators ==
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* Working on drafts, papers, grants, presentations &c
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** Lab [[Resources Document]] (NIH form)
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** Conventions for editing Google Docs - http://goo.gl/kSrS9
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** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
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** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
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** [[CRAMTOOLS and common directory]]
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<center>'''http://www.gersteinlab.org'''</center>
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* Computing
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** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
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** [[Gerstein Lab Computing in HPC]]
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** [[Gerstein Lab Openstack 2017]]
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** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]
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====PhD Studentships in Bioinformatics at Yale====
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* Calls, meetings, &c
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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].
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**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]])
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**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
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**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
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** Information on [[Meeting Invites]]
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**  [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])
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** [[Zoomrooms]] in BASS 434
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**[[Whiteboard camera system]] in BASS 434
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**[[IR remote-Logitech Harmony express]] in BASS 434
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====[[Summer Jobs & Undergraduate Researcher]]====
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* Some Useful University Policies
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** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
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** 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]
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** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
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** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3  Yale Purchasing Buy/Pay Matrix 3401.3]
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== Info for New People ==
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* Documents
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*[[General Information for New Undergraduates]] thinking about working in the lab
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** [[Uploading_documents]]
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* 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])
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== Info for Lab Members and Collaborators ==
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* Misc
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*[http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
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**[[Getting Mark's signature for documents]]
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*[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
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**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
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*[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
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**Prominent [[public wiki pages linked from elsewhere]]
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*[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
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**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
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*[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
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**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
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* [[Streamlining Draft Flow]] (Ideas for streamlining the process of drafting and submitting papers)
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**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
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** Way to list Mark's [[Affiliation]] on papers
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** [[Recommendation Letters]]
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** See [[xxmg at gersteinlab.org | xxmg@gersteinlab.org]] for correct address to use for paper correspondence.
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**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
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** Note that '''xxmg at bioinfo.mbb.yale.edu''' for paper correspondence is deprecated.
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** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
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* [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
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** 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]
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* [[Recommendation Letters]]
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** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
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* Lab [[Resources Document]] (NIH form)
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**[[OpenStack]]
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* [[Papers Page Code]]
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**[[IDP report]]
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* Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
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**[[PEC package preprints]]
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* Some Useful University Policies
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** 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]]
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** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
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* 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]
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* [http://maguro.cs.yale.edu:8000/Center_for_High_Performance_Computation_in_Biology_and_Biomedicine Yale High Performance Computing Center]
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* Information on [[what grant to charge something to]]
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* Information on [[Meeting Invites]]
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* [http://araman.mbgnet/nagios/ System Status] MBGNet LAN access only.
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Latest revision as of 01:58, 5 September 2019

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

More Info for New People

Info for Lab Members and Collaborators

Personal tools