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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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*Gerstein Lab '''[https://twitter.com/GersteinLab Twitter]'''
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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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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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*[[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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<HR>
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*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
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----
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== Other Stuff for the Public ==
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*[[FAQ]] (new) on programs
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*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
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*Prominent [[public wiki pages linked from elsewhere]]
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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]
== Info for New People ==
== Info for New People ==
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*[[General Information for New Undergraduates]] thinking about working in the lab
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* Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.
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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 ==
== Info for Lab Members and Collaborators ==
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*[http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
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* Working on drafts, papers, grants, presentations &c
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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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** Lab [[Resources Document]] (NIH form)
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*[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
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** Conventions for editing Google Docs - http://goo.gl/kSrS9
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*[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
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** Pointers on [[Streamlining Draft Flow]] (Ideas related to 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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*** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist]
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* [[Streamlining Draft Flow]] (Ideas for streamlining the process of drafting and submitting papers)
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** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
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** Way to list Mark's [[Affiliation]] on papers
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** [[CRAMTOOLS and common directory]]
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** See [[xxmg at gersteinlab.org | xxmg@gersteinlab.org]] for correct address to use for paper correspondence.
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** Note that '''xxmg at bioinfo.mbb.yale.edu''' for paper correspondence is deprecated.  
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* Computing
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* [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
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** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.  
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* [[Recommendation Letters]]
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** [[Gerstein Lab Computing in HPC]]
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* Lab [[Resources Document]] (NIH form)
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** [[Gerstein Lab Computing in GersteinLab West Campus]]
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* [[Papers Page Code]]
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** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]
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* Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
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* Calls, meetings, &c
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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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**Booking [[Meeting Room]]
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* Some Useful University Policies
* 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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** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]
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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]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
** 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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** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3  Yale Purchasing Buy/Pay Matrix 3401.3]
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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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* Documents
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* Information on [[Meeting Invites]]
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** [[Uploading_documents]]
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* [http://araman.mbgnet/nagios/ System Status] MBGNet LAN access only.
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** Letterhead templates (at http://wiki.gersteinlab.org/labinfo/index.php/Templates)
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* Misc
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**[[Getting Mark's signature for documents]]
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**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
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**Prominent [[public wiki pages linked from elsewhere]]
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**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
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**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
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**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
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** [[Recommendation Letters]]
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**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
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** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
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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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** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
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**[[OpenStack]]
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**[[IDP report]]
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**[[PEC package preprints]]
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**[[Summary of undergraduate involvement]]
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**Lab [http://bit.ly/mglab-folder google folder]
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**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]

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