GersteinInfo - User contributions [en]

Main Page

2026-01-22T14:18:54Z

Infoadmin:

[https://www.gersteinlab.org Gerstein Lab Home Page]

== Important Public Items ==
*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]] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab

__TOC__

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]]

<HR>

== Other Stuff for the Public ==
*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]

== 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.
* [[Glossary]] of terms.
* Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]

== 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 ==
* 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] ('''Proofsx57m''')
** [[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]

* 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]]

* 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]

* 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)

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[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)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** 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]
** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
**[[OpenStack]]
**[[IDP report]]
**[[PEC package preprints]]
**[[Summary of undergraduate involvement]]
**Lab [http://bit.ly/mglab-folder google folder]
**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]

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Pi at gersteinlab.org

2012-05-14T11:07:48Z

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* Use pi at gersteinlab.org address for paper correspondence.
** Contact the lab manager for access to the pi2 at gersteinlab.org account
** The lab manager (currently MF) will configure access on demand.
** More instructions for lab members can be found in the [http://wiki.gersteinlab.org/labinfo/Pi_at_gersteinlab.org private wiki].

*Important new points on using pi at gersteinlab
**Use the pi at gersteinlab.org up until the proofs. Once proofs are ready inform editor and switch to mark dot gerstein at yale.edu.
**When writing emails as pi at gersteinlab.org cc the email to pi at gersteinlab.org.
**You are responsible for checking pi at gersteinlab.org for emails regarding your paper.

Pi at gersteinlab.org

2012-05-14T11:07:23Z

Infoadmin:

* Use pi at gersteinlab.org address for paper correspondence.
** Contact the lab manager for access to the pi2 at gersteinlab.org account
** The lab manager (currently MF) will configure access on demand.
** More instructions for lab members can be found in the [http://wiki.gersteinlab.org/labinfo/Pi_at_gersteinlab.org private wiki].

*Important new points on using pi _at_ gersteinlab
**Use the pi at gersteinlab.org up until the proofs. Once proofs are ready inform editor and switch to mark dot gerstein at yale.edu.
**When writing emails as pi at gersteinlab.org cc the email to pi at gersteinlab.org.
**You are responsible for checking pi at gersteinlab.org for emails regarding your paper.

Pubmed query

2011-11-01T12:30:34Z

Infoadmin:

[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pubmed&dispmax=200&relpubdate=No%20Limit&term=%28%28Gerstein%20M%5BAuthor%5D%20NOT%20%281957%5Bdp%5D%20%3A%201990%5Bdp%5D%29%29%20NOT%2010787728%5BUID%5D%20NOT%2011744447%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2016081066%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2017270657%5BUID%5D%20NOT%2021243890%5BUID%5D%20NOT%2021406498%5BUID%5D%20NOT%2021945273%5BUID%5DOR%2015499007%5BUID%5D%20OR%2017571346%5BUID%5D%20OR%2017571346%5BUID%5D%20OR%208877505%5BUID%5D%20OR%208816770%5BUID%5D%20OR%207540695%5BUID%5D%20OR%207567918%5BUID%5D%20OR%207567918%5BUID%5D%20OR%207577841%5BUID%5D%20OR%207567917%5BUID%5D%20OR%207643385%5BUID%5D%20OR%208749848%5BUID%5D%20OR%208808580%5BUID%5D%20OR%208120887%5BUID%5D%20OR%208029203%5BUID%5D%20OR%208204609%5BUID%5D%20OR%207922041%5BUID%5D%20OR%207584390%5BUID%5D%20OR%208078776%5BUID%5D%20OR%208428572%5BUID%5D%20OR%208429559%5BUID%5D%20OR%208464069%5BUID%5D%20OR%208234227%5BUID%5D%20OR%208230220%5BUID%5D%20OR%201584800%5BUID%5D%20OR%202067013%5BUID%5D%20OR%2020981092%5BUID%5D%20OR%2021526222%5BUID%5D%29 Old Medline Query]

[http://oldpapers.gersteinlab.org/search/labquery.pl?query=default Old link to construct link above]

[http://papers.gersteinlab.org/NCBIData.xml Current NCBI XML File]

Pubmed query

2011-10-12T07:11:52Z

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Papers Page Code

2011-09-13T15:23:50Z

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==New Stuff==

[https://docs.google.com/spreadsheet/ccc?key=0AiiHlTECOi8edGhzSXlZZzEyRThQeDB6R0pRc0FvcGc&hl=en_US#gid=0 MBGLab--Papers-Master]

[https://docs.google.com/spreadsheet/ccc?key=0AiiHlTECOi8edDBCUUhtMFZzRFVMaVlxZ1JrNGp1b0E&hl=en_US#gid=0 Papers-Subjects]

==Automatic generation of publication documents from SpreadSheet==

====[http://papers.gersteinlab.org Return to index]====

<font size="3" face="arial, Helvetica, sans-serif"> '''Introduction and guidelines:''' All papers are defined by a unique "labid" such as "pgenes-nar" or "genome-transposon-nature". Ideally, the labid should contain the abbreviated subject and journal name as shown. To add a paper, you simply need to go to MBGLab--Papers-Master (Link above) , then fill in the corresponding columns. If you also want to add a new subject area, go to Papers-Subjects (Link above). After finishing adding new papers, go to [http://wiki.gersteinlab.org/labinfo/Main_Page private wiki] and find the rebuild link (under Papers / Manuscripts ), then click it.

Here is a list of the tags and their meanings:

<blockquote>
*Papers Master
<Labid> - id by which to refer to the article <br />
<PMID> - PubMed id<br />
<Title> - title of the article (If pubmed id exists, leave blank) <br />
<Citation> - citation of the article (author, journal, year, etc) (If pubmed id exists, leave blank)<br />
<preprint> - URL of the preprint file<br />
<subjects> - specifies the grant(s) funding the paper (e.g. "cegs,keck") (refer to Papers Subjects)<br />
<website> - supplemental website<br />
<Year> - published year of an article (must fill in) <br />
<footnote> - footnote of this article <br />
<website2> - second supplemental website<br />
*Papers Subject
<Category> - classification of research areas<br />
<LabID> -name of grants <br />
<Title> - brief description of grants <br />
<Website> - website of research grants <br />
<Html> - content appears on webpage <br />
</blockquote>

The tags under Papers Master can conceptually be divided into two groups: ones such as PMID and labitle, which serve to identify the paper, and tags such as website and subject which supply supplemental information about the paper. There are two ways to identify a paper (in order of decreasing precedence):

# PMID
# Title, Citation

You should always include the PMID if a paper is known to be listed in PubMed. Option 2 should be used for papers that are in press.

The other group of tags supplies additional information about the paper specified by the first group of tags. All of these tags are optional, however used of <tt><subjects></tt> and <tt><preprint> </tt> is strongly encouraged. (Please consult Mark for guidelines on citing grants.)
</font>

==Rebuild Link==
{|
|[http://wiki.gersteinlab.org/labinfo/Main_Page Rebuild Link on private wiki]
| align="center" |
|}

==Old Code Page==
Redirect [[Papers Page Code Old]]

==Old Papers Server==
[http://oldpapers.gersteinlab.org Old Papers]

[[Paper_search]]

Papers Page Code

2011-09-13T15:23:14Z

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Papers Page Code

2011-09-13T15:22:45Z

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Papers Page Code

2011-09-13T15:20:52Z

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Papers Page Code

2011-09-13T15:20:31Z

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Status of Lab Web Resources

2011-09-01T06:26:41Z

Infoadmin:

See the system status [http://netmon.gersteinlab.org/nagios/cgi-bin/status.cgi?servicegroup=publishedurls&style=detail page] (login with user "view",
with no password) for an overview of most of our servers.

Many of the our sites are coupled to publications. These are indicated by the website tag on our [http://papers.gersteinlab.org publication page] . In particular, here's an list from early 2010 of [[Analysis_of_Lab_Publications|all websites referred to on the papers page]].

We have many sites that we are responsible for (>150 Unique websites associated with lab papers 9-May-2010). We know that some sites referred to in our papers are down transiently (or permanently). Here's a listing of sites with known problems:

Internal server that has been down for a long time
http://yeasthub.gersteinlab.org

Broken external links (out of our control):
http://zerlina.ingentaselect.com/vl=9024539/cl=83/nw=1/rpsv/cw/mal/10665277/v11n4/contp1-1.htm
http://www-smi.stanford.edu/projects/helix/LPFC
http://www.cbio.mskcc.org/~jansen/comb/
http://www.nature.com/nsb/structural_genomics
http://purelight.biology.yale.edu:8080/servlets-examples/procat.html

Status of Lab Web Resources

2011-09-01T06:26:04Z

Infoadmin:

See the system status [http://netmon.gersteinlab.org/nagios/cgi-bin/status.cgi?servicegroup=publishedurls&style=detail page] (login with
user "view", with no password) for an overview of most of our servers.

Many of the our sites are coupled to publications. These are indicated by the website tag on our [http://papers.gersteinlab.org publication page] . In particular, here's an list from early 2010 of [[Analysis_of_Lab_Publications|all websites referred to on the papers page]].

We have many sites that we are responsible for (>150 Unique websites associated with lab papers 9-May-2010). We know that some sites referred to in our papers are down transiently (or permanently). Here's a listing of sites with known problems:

Internal server that has been down for a long time
http://yeasthub.gersteinlab.org

Broken external links (out of our control):
http://zerlina.ingentaselect.com/vl=9024539/cl=83/nw=1/rpsv/cw/mal/10665277/v11n4/contp1-1.htm
http://www-smi.stanford.edu/projects/helix/LPFC
http://www.cbio.mskcc.org/~jansen/comb/
http://www.nature.com/nsb/structural_genomics
http://purelight.biology.yale.edu:8080/servlets-examples/procat.html

Lab Address

2011-08-29T10:16:31Z

Infoadmin: /* Main Room Numbers */

==PI Contact Address==
Mark Gerstein
([http://contact.gerstein.info contact.gerstein.info])

==Admin Assistant==
Send messages for the assistant to adminasst (at) gersteinlab.org . The current administrative assistant for the lab is Mary Barney.

==Main Room Numbers==
*Bass 426: 203 432 8972
*Bass 428: 203 432 5065
*Bass 437: 203 432 5405
*Gibbs 352: 203 432 8771 (near window), 203 432 5612 (near door)
*Gibbs 370: 203 432 6337
*[[Mihali Felipe]] (sysadm): 203 432 8771 (Emergencies only: 203 623-8873)

==Other Useful Numbers==
*Gibbs 362A (Core Conference Room): 203 432 6191
*Gibbs 371 (Core Labs Terminal Room)): 203 432 5615
*Gibbs 355E (Art Perlo, Core Sysadm): 203 432 5614
*Gibbs 355D (David Keller, Core Sysadm2): 203 432 5743
*Bass 432 : 203 432 8189
*Bass 432A (Mark Gerstein): 203 432 6105
*Bass 424: conference room on Bass 4th floor
*Bass 425: 203 432 5599
*AKW 204: 203 432 1209
*AKW 206: office in AKW that Mark occasionally uses (changed from 205)

==Laboratory Floor Plans==
*[http://www.gersteinlab.org/people/figures/bass-west-4th-fl-more.gif Bass Fourth Floor]
*[http://www.gersteinlab.org/people/figures/gibbs-core-plan-2.gif Gibbs Core Facility]
*[http://docs.google.com/Present?docid=dzjxmkd_0gpx33s&fs=true Current Desk Assignments]

==Directions and Maps==
We're mostly located in the fourth floor of the [http://www.gersteinlab.org/people/bass.jpg Bass Building], but also have some outposts in Gibbs and AKW. The Bass Center is located at 266 Whitney Avenue. It faces the Biology department in Klein Tower. Click [http://www.gersteinlab.org/people/gerstein-map.html here] for an interactive satellite image of the Science Hill area from Google maps. Follow the link for a interactive [http://www.facilities.yale.edu/campus/Imapnew.asp campus map] and information for the [http://www.facilities.yale.edu/Campus/building1.asp?lstbldg=1030&sec=3 Bass Center] from buildings & grounds.

General [http://www.yale.edu/directions.html Directions] to Yale University are posted on the University webserver. These include a detailed University [http://www.yale.edu/yaleinfo/maps/5.html map] locating the Bass building in the Science Hill area. Directions locating the Bass building on Science Hill is available [http://www.gersteinlab.org/people/directions.html here]. (Some of these maps are locally [http://bioinfo.mbb.yale.edu/~mbg/yale-maps mirrored]; in particular, a [http://bioinfo.mbb.yale.edu/~mbg/yale-maps/ConnAndVicinityReliefMap.gif relief map] of Connecticut and a map of the [http://bioinfo.mbb.yale.edu/~mbg/yale-maps/TownsOfGreaterNewHaven.gif towns] in the New Haven area).

==Rail==
[http://www.mta.nyc.ny.us/mnr/ Metro-North] and [http://www.amtrak.com/ Amtrak] service to New Haven (Taxis available at station.)

==Driving and Parking==
===From Boston===
#Take Mass Pike to Interstate 84.
#Take Interstate 84 South to Hartford.
#Take Interstate 91 South to New Haven.
#Take Exit 3 off of Interstate 91.
#Turn right at the stoplight at the end of the exit ramp onto Orange Street.
#Turn left onto Humphrey Street at next stoplight.
#Proceed through the next stoplight into the parking lot (Lot 16).

===From New York===
#Take Interstate 95 North to Interstate 91 at New Haven
#Take exit 3 off Interstate 91.
#Turn right at the stoplight at the end of the exit ramp onto Orange Street.
#Turn left onto Humphrey Street at next stoplight.
#Proceed through the next stoplight into the parking lot (Lot 16).
(Before getting on 95, it's nice to take the Merritt. You might want to follow this [http://www.gersteinlab.org/people/ny-to-ct.gif route].)

===Parking===
For parking, visitors should park in lot 16, which is the first right after entering the parking lot at Science Hill at the [http://maps.yahoo.com/py/maps.py?Pyt=Tmap&YY=7302&addr=266%20Whitney%20Avenue&city=New%20Haven&state=CT&slt=41.3180&sln=-72.9199&zip=06520&mag=1&cs=9&newmag=10 intersection of Whitney and Humphrey]. The department has one-day parking passes for this lot. Also see the Yale [http://housing-server.hgs.yale.edu/ParkingandTransit/directions.html Parking and Transit] web pages.

==Other Stuff==
[http://yp.yahoo.com/py/ypResults.py?Pyt=Tmap&YY=24974&addr=266%20Whitney%20Avenue&city=NEW%20HAVEN&state=CT&zip=06520&slt=&sln=&cs=&stp=y&stx=8903827&btype=default Yahoo: Nearby Restaurants], [http://maps.yahoo.com/py/maps.py?Pyt=Tmap&YY=28780&addr=266%20Whitney%20Avenue&city=New%20Haven&state=CT&slt=41.3180&sln=-72.9199&zip=06520&mag=10&cs=9&newmag=9 Map of Bass Area], [http://yp.yahoo.com/py/ypMap.py?Pyt=Tmap&YY=8688&addr=266%20Whitney%20Avenue&city=NEW%20HAVEN&state=CT&country=US&slt=41.3180&sln=-72.9199&zip=06520&mag=9&cs=9&stx=7737307&stp=y&ycat=7737307&l=11&tuid=566518&tq=8&btype=default Colony Inn] (nearby hotel), [http://yp.yahoo.com/py/ypResults.py?Pyt=Tmap&YY=32031&addr=266%20Whitney%20Avenue&city=NEW%20HAVEN&state=CT&zip=06520&slt=&sln=&cs=9&stp=y&stx=8014796&btype=default Taxi] services.

Status of Lab Web Resources

2011-08-27T21:19:38Z

Infoadmin:

See the system status [http://netmon.gersteinlab.org/nagios/cgi-bin/status.cgi?servicegroup=publishedurls&style=detail page] (login with user "view", with no password) for an overview of most of our servers.

Many of the our sites are coupled to publications. These are indicated by the website tag on our [http://papers.gersteinlab.org publication page] . In particular, here's an list from early 2010 of [[Analysis_of_Lab_Publications|all websites referred to on the papers page]].

We have many sites that we are responsible for (>150 Unique websites associated with lab papers 9-May-2010). We know that some sites referred to in our papers are down transiently (or permanently). Here's a listing of sites with known problems:

Internal server that has been down for a long time
http://yeasthub.gersteinlab.org

Broken external links (out of our control):
http://zerlina.ingentaselect.com/vl=9024539/cl=83/nw=1/rpsv/cw/mal/10665277/v11n4/contp1-1.htm
http://www-smi.stanford.edu/projects/helix/LPFC
http://www.cbio.mskcc.org/~jansen/comb/
http://www.nature.com/nsb/structural_genomics
http://purelight.biology.yale.edu:8080/servlets-examples/procat.html

Main Page

2011-08-10T09:51:56Z

Infoadmin:

This wiki hosts general, public information about the

{| style="color:white"
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="blue"|
| width="1" bgcolor="blue"|
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="white"| [http://gersteinlab.org '''Gerstein Lab''']
| width="1" bgcolor="blue"|
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="blue"|
| width="1" bgcolor="blue"|
|}

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 ==
*Public [[Documents]] about the lab
*[[FAQ]] (new) on programs
*Lab [[Calendar]]
*[http://www.gersteinlab.org/index.html.1jun11 Old version] of lab homepage
*[[Permissions]]
*Prominent [[public wiki pages linked from elsewhere]]

== Info for New People ==
*[[General Information for New Undergraduates]] thinking about working in the lab
* [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab Information] for <B>new people</B> starting in the lab from the private wiki
* [http://wiki.gersteinlab.org/labinfo/Staff People] to look for to get oriented
* About [http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure Group Meetings and JClubs]

== Info for Lab Members and Collaborators ==
*[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)
* 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]] 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]
* 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://netmon.gersteinlab.org/nagios/cgi-bin/status.cgi?host=all System Status]
* [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])

Main Page

2011-08-09T21:55:08Z

Infoadmin:

This wiki hosts general, public information about the

{| style="color:white"
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="blue"|
| width="1" bgcolor="blue"|
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="white"| [http://gersteinlab.org '''Gerstein Lab''']
| width="1" bgcolor="blue"|
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="blue"|
| width="1" bgcolor="blue"|
|}

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 ==
*Public [[Documents]] about the lab
*[[FAQ]] (new) on programs
*Lab [[Calendar]]
*[http://www.gersteinlab.org/index.html.1jun11 Old version] of lab homepage
*[[Permissions]]
*Prominent [[public wiki pages linked from elsewhere]]

== Info for New People ==
*[[General Information for New Undergraduates]] thinking about working in the lab
* [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab Information] for <B>new people</B> starting in the lab from the private wiki
* [http://wiki.gersteinlab.org/labinfo/Staff People] to look for to get oriented
* About [http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure Group Meetings and JClubs]

== Info for Lab Members and Collaborators ==
*[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)
* 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]] 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]
* 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://netmon.gersteinlab.org/nagios/ System Status]
* [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])

Mihali Felipe

2011-06-18T12:47:03Z

Infoadmin:

[http://wiki.gersteinlab.org/labinfo/Mihali_Felipe Lab Pages (internal)]

[http://homes.gersteinlab.org/people/mihali MB&B]

[http://pantheon.yale.edu/~mihali Yale]

Resources Document

2011-06-16T15:09:39Z

Infoadmin:

Information about lab resources can be found here:
*[https://docs.google.com/document/pub?id=12gDLHs29wIQxJkhGVx-Ye3uES47um86BlzBk4C9wbEA NIH resources document (currently version, gdoc will be updated)]
*[[Image:GersteinLab-Resources-21Oct08.doc|NIH|NIH resources document (revised 21Oct2008)]]
*[[Image:GersteinLab-Resources-1Sep07.doc|NIH|NIH resources document (1Sept2007)]]

Resources Document

2011-06-16T12:20:36Z

Infoadmin:

Information about lab resources can be found here:
*[https://docs.google.com/document/d/12gDLHs29wIQxJkhGVx-Ye3uES47um86BlzBk4C9wbEA NIH resources document (currently version, gdoc will be updated)]
*[[Image:GersteinLab-Resources-21Oct08.doc|NIH|NIH resources document (revised 21Oct2008)]]
*[[Image:GersteinLab-Resources-1Sep07.doc|NIH|NIH resources document (1Sept2007)]]

Search

2011-03-23T12:00:06Z

Infoadmin:

* Searchable wiki of [http://wiki.gersteinlab.org/pubinfo Lab Information]

==FAQs==

* [http://faqs.gersteinlab.org/ FAQs]
* [http://bioinfo.mbb.yale.edu/pipermail/faq/ old FAQs]

==Search Engines==

Here are some examples:
[http://hub.gersteinlab.org/id/6ldh 6ldh]

Search

2011-03-22T08:40:19Z

Infoadmin:

* Searchable wiki of [http://wiki.gersteinlab.org/pubinfo Lab Information]

==FAQs==

* [http://faqs.gersteinlab.org/ FAQs]
* [http://bioinfo.mbb.yale.edu/pipermail/faq/ old FAQs]

==Search Engines==

Search

2011-03-16T09:49:54Z

Infoadmin:

* Searchable wiki of [http://wiki.gersteinlab.org/pubinfo Lab Information]

==FAQs==

* [http://faqs.gersteinlab.org/ FAQs]
* [http://bioinfo.mbb.yale.edu/pipermail/faq/ old FAQs]

==Search Engines==

<html>

<TABLE CELLPADDING=0 CELLSPACING=0 BORDER=0>
<TR ALIGN=left VALIGN=center>
<TD width=750>
<form method="GET" action="http://bioinfo.mbb.yale.edu/search.cgi">
<H2>
<FONT FACE="sans-serif,helvetica,arial">
Search
<input size=10 maxlength=150 name="q">
</FONT>
<FONT SIZE=-1 FACE="sans-serif,helvetica,arial">
<select name="option" size="1">
<option value="Lab Sites">Lab Sites</option>

<option value="Linkhub">Linkhub</option>
<option value="Gene or PDB ID">Gene or PDB ID (old)</option>
<option value="Text on this site">Text on this site</option>
<option value="Pages linking us">Pages linking us</option>
</select>
<input type="submit" value="Go!">
</FONT>
</FORM>
</TD><TD ALIGN=left width=275>
<FONT SIZE=-2><BR>E.G.
<a href="http://hub.gersteinlab.org/id/6ldh">6ldh</A>,
<a href="http://hub.gersteinlab.org/id/YOR133W">YOR133W</a>,

<a href="http://bioinfo.mbb.yale.edu/genome/search/superlink.cgi?id=Rv1655">Rv1655</a>,
<a href="http://bioinfo.mbb.yale.edu/genome/search/superlink.cgi?id=d4hhba_">d4hhba_</A>
<a href="http://bioinfo.mbb.yale.edu/genome/search/superlink.cgi?id=LacZ">LacZ</a>
 <BR>(Special <A HREF="http://bioinfo.mbb.yale.edu/search">Search Page</A> and Link <A HREF="http://hub.gersteinlab.org">Hub</A> search page)</H2>
</FONT>

</FORM>

</TD></TR></TABLE>

</html>

Search

2011-03-16T09:49:21Z

Infoadmin:

* Searchable wiki of [http://wiki.gersteinlab.org/pubinfo Lab Information]

==FAQs==

* [http://faqs.gersteinlab.org/ FAQs]
* [http://bioinfo.mbb.yale.edu/pipermail/faq/ old FAQs]

==Search Engines==

<TABLE CELLPADDING=0 CELLSPACING=0 BORDER=0>
<TR ALIGN=left VALIGN=center>
<TD width=750>
<form method="GET" action="http://bioinfo.mbb.yale.edu/search.cgi">
<H2>
<FONT FACE="sans-serif,helvetica,arial">
Search
<input size=10 maxlength=150 name="q">
</FONT>
<FONT SIZE=-1 FACE="sans-serif,helvetica,arial">
<select name="option" size="1">
<option value="Lab Sites">Lab Sites</option>

<option value="Linkhub">Linkhub</option>
<option value="Gene or PDB ID">Gene or PDB ID (old)</option>
<option value="Text on this site">Text on this site</option>
<option value="Pages linking us">Pages linking us</option>
</select>
<input type="submit" value="Go!">
</FONT>
</FORM>
</TD><TD ALIGN=left width=275>
<FONT SIZE=-2><BR>E.G.
<a href="http://hub.gersteinlab.org/id/6ldh">6ldh</A>,
<a href="http://hub.gersteinlab.org/id/YOR133W">YOR133W</a>,

<a href="http://bioinfo.mbb.yale.edu/genome/search/superlink.cgi?id=Rv1655">Rv1655</a>,
<a href="http://bioinfo.mbb.yale.edu/genome/search/superlink.cgi?id=d4hhba_">d4hhba_</A>
<a href="http://bioinfo.mbb.yale.edu/genome/search/superlink.cgi?id=LacZ">LacZ</a>
 <BR>(Special <A HREF="http://bioinfo.mbb.yale.edu/search">Search Page</A> and Link <A HREF="http://hub.gersteinlab.org">Hub</A> search page)</H2>
</FONT>

</FORM>

</TD></TR></TABLE>

MBG-Profile

2011-03-15T10:06:59Z

Infoadmin:

* Here is a 50 word description of my research (31-Aug-2009)

Dr. Gerstein is the Albert Williams Professor of Biomedical Informatics, Molecular Biophysics &
Biochemistry and Computer Science at Yale University. His research involves applying quantitative
approaches such as data mining and simulation to problems in molecular biology. He is specifically
interested in human genome annotation, molecular networks, and macromolecular geometry.

* Here is a [[short 150-word profile]]

* Longer Wiki Description of [[Mbg-research]]

(out of date as of Aug-2009)

* There are many profile pages that are associated with me. Most of these are out of date.

* Main Page

http://gersteinlab.org/about

* Extra Stuff that I've seem to have accumulated

[http://www.google.com/profiles/bluehat Google] (not very used Google profile page)

[http://www.zoominfo.com/Search/ReferencesView.aspx?PersonID=14758619 ZoomInfo] (contains comprehensive listing of articles referring to the lab)

[http://genealogy.math.ndsu.nodak.edu/id.php?id=69445 Math Genealogy Project]

[http://info.med.yale.edu/bbs/faculty/ger_ma.html BBS Page]

[http://bioinfo.mbb.yale.edu/about/nih-style-full-cv-apr-05.doc Complete CV, MS Word format]

[http://www.gersteinlab.org/about/cv/ NIH-style Full CV with Publications]

[http://www.gersteinlab.org/about/cv-nih-format.htm NIH-style HTML header]

More research descriptions:
* [http://expertise.cos.com/cgi-bin/exp.cgi?id=414253 COS]
* [http://www.gersteinlab.org/about/short-bio.txt Micro-BIO]
* [http://www.mbb.yale.edu/faculty/pages/gerstein.html MB&B]
* [http://www.cs.yale.edu/people/gerstein.html CS] (last updated Sept. 2009)
* Older Description (010108) with figures and many file formats:
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108.doc doc]
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108-figs.pdf pdf]
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108-figs.ppt ppt]
* [http://www.gersteinlab.org/about/long-descrip.pdf An even older (1999) version in pdf]

==More Old Stuff==

Research Program [http://papers.gersteinlab.org/about/sum2006 2006], [http://papers.gersteinlab.org/papers/papers-research.shtml 2002a],
[http://bioinfo.mbb.yale.edu/about/sum/res-sum-020128.htm 2002b], [http://papers.gersteinlab.org/about/sum2001 2001]

Description of our research featured in [http://pubs.acs.org/cen/coverstory/7839/7839scit1.html]C&E News ([http://www.gersteinlab.org/about/7839scit1.html local])

==Publications==
* Google Scholar: http://scholar.google.ca/scholar?q=author:gerstein-m

Mihali Felipe

2011-03-06T22:05:31Z

Infoadmin:

[http://wiki.gersteinlab.org/labinfo/Mihali_Felipe Lab Pages (internal)]

[http://homes.gersteinlab.org/people/Mihali MB&B]

[http://pantheon.yale.edu/~mihali Yale]

Lecture Today

2011-03-02T12:24:16Z

Infoadmin: Created page with 'Check back for information about Mark Gerstein's slides for today's lecture.'

Check back for information about Mark Gerstein's slides for today's lecture.

Ortholog Resources

2011-03-01T23:08:19Z

Infoadmin: Created page with '* Current Status Below are version 1 of some modENCODE ortholog resources. Its main page is http://www.modencode.org/ These are only for worm, fly and human. They do not yet com…'

* Current Status

Below are version 1 of some modENCODE ortholog resources. Its main page is http://www.modencode.org/ These are only for worm, fly and human. They do not yet completely use the [http://wiki.modencode.org/project/index.php/Reference_genes_and_transcripts Reference genes and transcripts].
The paper referring these builds can be found here http://papers.gersteinlab.org/

Future plans involve making more use of the reference sets and incorporating yeast.

* Cross Comparison Results '''(Use these!)'''

We were able to use the different ortholog pairs and triplets that we had in order to look at how much overlap there was between the different ortholog resources. The file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_fly.op.3 human_fly.op.3] contains the human-fly orthologs that are reported by all three ortholog resources. Similarly [http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_fly.op.2 human_fly.op.2] contains the human-fly ortholog pairs that have been reported in at least two of the aforementioned data resources. The file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_fly.op.3 human_fly.op.1] has the human-fly ortholog pairs that were found in only one of the resources. The same analysis was done for the human-worm and worm-fly ortholog pairs, as well as the human-worm-fly triplets. '''Use the file containing all three resources for the list of most conservative ortholog pairs and triplets. The other files can be added if more pairs for the list are desired. The files are located below.'''

{|border="1" cellpadding="3" cellspacing="0" align="left"
|-
!File Name
!Number of ortholog pairs
!
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/fly_worm.op.3 fly_worm.op.3]
|1,226
|'''Use for most conservative fly-worm pairs'''
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_fly.op.3 human_fly.op.3]
|1,955
|'''Use for most conservative human-fly pairs'''
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_worm.op.3 human_worm.op.3]
|2,538
|'''Use for most conservative human-worm pairs'''
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Triplet/worm_human_fly.triplet.3 worm_human_fly.triplet.3]
|829
|'''Use for most conservative worm-human-fly triplets'''
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/fly_worm.op.2 fly_worm.op.2]
|4,060
|
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_fly.op.2 human_fly.op.2]
|5,962
|
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_worm.op.2 human_worm.op.2]
|5,109
|
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Triplet/worm_human_fly.triplet.2 worm_human_fly.triplet.2]
|6856
|
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/fly_worm.op.1 fly_worm.op.1]
|9,927
|
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_fly.op.1 human_fly.op.1]
|12,653
|
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Results/human_worm.op.1 human_worm.op.1]
|99,260
|
|-
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Triplet/worm_human_fly.triplet.1 worm_human_fly.triplet.1]
|34,744
|
|}
<br/>

Example of how the files were created:
Suppose in Inparanoid we see an ortholog group that consists of 5 genes ''human-1, human-2, human-3, worm-1, fly-1''
In TreeFam we see 4 of the 5 genes, ''human-1, human-2, worm-1, fly-1'' in the same ortholog group.
In OrthoMCL none of the 5 genes exists in an ortholog group. These pairs and triplets would be assigned to the op.2 files

We would build the following:

2 human-worm-fly ortholog triplets assigned to op.2:
(''human-1, worm-1, fly-1'')
(''human-2, worm-1, fly-1'')

2 human-worm ortholog pairs assigned to op.2:
(''human-1, worm-1'')
(''human-2, worm-1'')

2 human-fly ortholog pairs assigned to op.2:
(''human-1, fly-1'')
(''human-2, fly-1'')

1 worm-fly ortholog pair assigned to op.2:
(''worm-1, fly-1'')
In this case of worm-fly pair, the number of triplets is larger then the number of pairs

If we change the assumption and an ortholog group exists in OrthoMCL that consists of ''human-1, human-2, worm-2''. There will be some changes in assignments from op.2 to op.3.

We would build the following:
2 human-worm ortholog pairs, assigned to op.3. There will be 0 pairs in op.2:
(''human-1, worm-1'')
(''human-2, worm-1'')

2 human-worm-fly triplets, assigned to op.2:
(''human-1, worm-1, fly-1'')
(''human-2, worm-1 , fly-1'')

2 human-fly ortholog pairs assigned to op.2:
(''human-1, fly-1'')
(''human-2, fly-1'')

1 worm-fly ortholog pair assigned to op.2:
(''worm-1, fly-1'')

In summary, the "op.3" files means the ortholog pair exists in Inparanoid, OrthoMCL, and TreeFam, three independent ortholog resources, which would be the most conservative. If the op.1, op.2, op.3 were combined together, there would be more ortholog pairs.

==Resources used to build the ortholog pairs and triplets==

*InParanoid

Data Resource and Website:
http://inparanoid.sbc.su.se/download/current/sqltables/

Files downloaded:<br/>
[http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.ensHOMSA.fa-modDROME.fa sqltable.ensHOMSA.fa-modDROME.fa] File containing the huamand and fly proteins <br/>
[http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.ensHOMSA.fa-modCAEEL.fa ensHOMSA.fa-modCAEEL.fa] File containing human and worm proteins <br/>
[http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.modCAEEL.fa-modDROME.fa modCAEEL.fa-modDROME.fa] File containing worm and fly proteins<br/>

Date of Download: April 6, 2009

Analysis of downloaded files:<br/>
1. In table [http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.ensHOMSA.fa-modDROME.fa sqltable.ensHOMSA.fa-modDROME.fa] 9,516 human proteins and 6,351 fly proteins are assigned into 5,586 ortholog groups.<br/>
2. In table [http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.ensHOMSA.fa-modCAEEL.fa ensHOMSA.fa-modCAEEL.fa] 8,900 human proteins and 5,825 worm proteins are assigned into 4,658 ortholog groups.<br/>
3. In table [http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.modCAEEL.fa-modDROME.fa modCAEEL.fa-modDROME.fa] 5,296 fly proteins and 5,367 worm proteins are assigned into 4,333 ortholog groups.<br/>
{|border="1" cellpadding="3" cellspacing="0" align="left"
|-
!File Name
!Human Proteins
!Worm Proteins
!Fly Protein
!Ortholog Groups
|-
|[http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.ensHOMSA.fa-modDROME.fa sqltable.ensHOMSA.fa-modDROME.fa]
|9,516
|n/a
|6,351
|5,586
|-
|[http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.ensHOMSA.fa-modCAEEL.fa ensHOMSA.fa-modCAEEL.fa]
|8,900
|5,825
|n/a
|4,658
|-
|[http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.modCAEEL.fa-modDROME.fa modCAEEL.fa-modDROME.fa]
|n/a
|5,367
|5,296
|4,333
|}
<br/>

4. Based on these 3 tables, we built 12,336 human-fly ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/InParanoid/ip.raw.human_fly Inparanoid_raw_human_fly], 113,805 human-worm ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/InParanoid/ip.raw.human_worm Inparanoid_raw_human_worm] and 10,321 fly-worm ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/InParanoid/ip.raw.fly_worm Inparanoid_raw_fly_worm]. We also built 10594 worm_human_fly ortholog triplets in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/Triplet/IP.worm_human_fly.triplet IP.worm_human_fly.triplet]<br/>
5. There is an issue with the worm data file. It contains many more protein IDs, which leads to the higher number of worm ortholog pairs.
Mapping to Reference Protein IDs and Summary:<br/>
To allow cross comparison, human and fly proteins IDs are mapped to the current Ensembl (53) protein IDs, and WormBase IDs are mapped to WormPep IDs, by using BioMart. If a human protein ID no longer exists in Ensembl, all ortholog pairs involved are removed. The ID mapping files are located under the head ID mapping at the end of the page. After mapping, we got 10,834 human-fly ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/InParanoid/IP.human_fly.pairs Inparanoid_human_fly_pairs], 96,724 human-worm ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/InParanoid/IP.human_worm.pairs Inparanoid_human_worm_pairs] and 8,876 fly-worm ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/InParanoid/IP.fly_worm.pairs InParanoid_fly_worm_pairs].

*OrthoMCL<br/>

Data Resource and Website:
http://www.orthomcl.org/common/downloads/2/

Files Downloaded:
[http://www.orthomcl.org/common/downloads/2/groups_orthomcl-2.txt.gz groups_orthomcl-2.txt.gz] File containing the different ortholog groups <br/>

Date of Download:
April 06, 2009

Analysis of downloaded files:<br/>
1. From [http://www.orthomcl.org/common/downloads/2/groups_orthomcl-2.txt.gz groups_orthomcl-2.txt.gz], we retrieved the following:<br/>
{|border="1" cellpadding="3" cellspacing="0" align="left"
|-
!Species
!Number of proteins
!Attached File Name
|-
|Human
|19,635
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/om.human.pro.raw OrthoMCL_raw_human]
|-
|Fly
|11,158
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/om.fly.pro.raw OrthoMCL_raw_fly]
|-
|Worm
|17,411
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/om.worm.pro.raw OrthoMCL_raw_worm]
|-
|In total
|48,204
|
|}
<br/>

2. Human proteins are identified by Ensembl protein ID. Fly protein IDs are from FlyBase and worm protein IDs are from WormBase.<br/>
3. Selecting from [http://www.orthomcl.org/common/downloads/2/groups_orthomcl-2.txt.gz groups_orthomcl-2.txt.gz] for the groups which contain proteins from at least two human, fly and worm species, we retrieved 6,467 ortholog groups, including 9,505 human proteins, 7,258 fly proteins and 5,931 worm proteins [http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/om.human_fly_worm.groups.raw OrthoMCL_raw_human_fly_worm_groups].<br/>
4. Based on these 6,467 ortholog groups, we built 14,556 human-fly ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/om.raw.human_fly OrthoMCL_raw_human_fly], 11,623 human-worm ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/om.raw.human_worm OrthoMCL_raw_human_worm] and 9,255 fly-worm ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/om.raw.fly_worm OrthoMCL_raw_fly_worm]. We also built 29481 human-worm-fly triplets [http://archive.gersteinlab.org/proj/orthologs/Orthologs/Triplet/OM.worm_human_fly.triplet OM.worm_human_fly.triplet ]

Mapping to Reference Protein IDs and Summary:<br/>
To allow cross comparison, human and fly protein IDs are mapped to the current Ensembl (53) protein IDs, and WormBase IDs are mapped to WormPep IDs, using BioMart. If a human protein ID no longer exists in Ensembl, all ortholog pairs involved are removed. The ID mapping files are located under the heading ID mapping at the end of the page. After mapping, we got 12,784 human-fly ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/OM.human_fly.pairs OrthoMCL_human_fly_pairs], 9,979 human-worm ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/OM.human_worm.pairs OrthoMCL_human_worm_pairs] and 8,047 fly-worm ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/OrthoMCL/OM.fly_worm.pairs OrthoMCL_fly_worm_pairs]<br/>

*TreeFam<br/>

Data Resource and Website:
ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/

Files Downloaded:<br/>
[ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/genes.txt.table.gz genes.txt.table.gz] Table containing the genes<br/>
[ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/species.txt.table.gz species.txt.table.gz] Table containing the different species<br/>
[ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/fam_genes.txt.table.gz fam_genes.txt.table.gz] Table showing the association between the genes' families <br/>
[ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/ortholog.txt.table.gz ortholog.txt.table.gz] Table containing the orthologs <br/>

Date of Download:
April 06, 2009

Analyses of downloaded Files:<br/>
1. From [ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/genes.txt.table.gz genes.txt.table.gz], we retrieved the following:
{|border="1" cellpadding="3" cellspacing="0" align="left"
|-
!Species
!Number of proteins
!Attached File Name
|-
|Human
|46,810
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.human.genes.raw human.genes.raw]
|-
|Fly
|19,789
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.fly.genes.raw fly.genes.raw]
|-
|Worm
|20,151
|[http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.worm.genes.raw tf.worm.genes.raw]
|-
|In total
|86,750
|
|}
<br/>

TreeFam was built on protein alignments. Based on the three files, our understanding is that each record is one transcription, and one gene could correspond to multiple transcripts, thus multiple records. We interpret one transcription as corresponding to one protein.

2. [ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/fam_genes.txt.table.gz fam_genes.txt.table.gz] presents the association of the genes’ family (both TreeFamA and TreeFamB). 803,408 genes were assigned to 16,141 gene families. Members of the same family should then be regarded as orthologs (together with in-paralogs). However, we found 204,845 IDs in this table that have no records in table genes.txt.table. We attached these 204,845 IDs in the file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.question_gfam.ids question_gfam.ids].

3. Ortholog pairs.

3.1 From table [ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/fam_genes.txt.table.gz fam_genes.txt.table.gz]<br/>
Selecting from table [ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/genes.txt.table.gz genes.txt.table.gz], the families containing human, fly and worm records (records are the total of 86,750 IDs), we got 8436 TreeFam families, and 7501 of them contains records from only one of the three species (this 8436 families are in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.human_fly_worm.fam_genes.raw human_fly_worm.fam_genes.raw]. The 935 families left containing records from more than one the three species are in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.human_fly_worm.fam_genes.all human_fly_worm.fam_genes.all]. From these 935 families, we got 2861 human-fly ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.fam_genes.human_fly tf.fam_genes.human_fly], 194 human-worm ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.fam_genes.human_worm fam_genes.human_worm] and only 27 fly-worm ortholog pairs are in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.fam_genes.fly_worm tf.fam_genes.fly_worm]. We also built 10872 human-worm-fly triplets [http://archive.gersteinlab.org/proj/orthologs/Orthologs/Triplet/TF.worm_human_fly.triplet TF.worm_human_fly.triplet].

3.2 From [ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/ortholog.txt.table.gz ortholog.txt.table.gz]<br/>
7,111,245 ortholog pairs are listed in this table, although we do not know how this table was created. From this table, we retrieved 15,004 human-fly ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.ortho_table.human_fly tf.ortho_table.human_fly], 14, 768 human-worm ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.ortho_table.human_worm tf.ortho_table.human_worm] and 12,544 fly-worm ortholog pairs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.ortho_table.fly_worm tf.ortho_table.fly_worm]. We did not do further filtering by the provided bootstrap value.

Mapping to Ensembl Protein IDs and Summary:<br/>
We used data from 3.2 as ortholog pairs from TreeFam: 15,004 human-fly, 14,768 human-worm and 12,544 fly-worm gene pairs. This includes 12,146 human IDs, 8,557 fly IDs, and 7,778 worm IDs from table [ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/genes.txt.table.gz genes.txt.table.gz]. Mapping the 12,146 human IDs to Ensembl protein ID (Ensembl 53, BioMart, transcript ID to protein ID), we got 11,433 Ensembl protein IDs in file [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.id_maping.human tf.id_mapping.human]. From 8,557 fly IDs, we got 4,588 fly Ensembl protein IDs (Ensembl 53, BioMart, Associated Transcript Name to protein ID, attached as [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.id_maping.fly tf.id_mapping.fly]. From 7,778 worm IDs, we got 6,308 WormBase peptide IDs (Ensembl 53, BioMart, transcript ID to WormPep ID, attached [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/tf.id_maping.worm tf.id_mapping.worm]. After mapping, we got 6,824 human-fly ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/TF.human_fly.pairs TF.human_fly.pairs], 10,389 human-worm ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/TF.human_worm.pairs TF.human_worm.pairs] and 4,802 fly-worm ortholog pairs [http://archive.gersteinlab.org/proj/orthologs/Orthologs/TreeFam/TF.fly_worm.pairs TF.fly_worm.pairs].

*ID mapping<br/>
In order to allow for cross comparison, we mapped the different protein IDs using the Ensemble protein IDs and the WormBase ID using BioMart

[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Mapping/fly.ensembl.idmapping fly_ensembl_idmapping] ID mapping using fly Ensemble ID and the Associated Transcript Name <br/>
[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Mapping/flybase.ensembl.idmapping flybase_ensembl_idmapping] ID mapping using fly Ensembl gene IDs and FlyBase protein IDs<br/>
[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Mapping/worm.ensembl.idmapping worm_ensembl_idmapping ] ID mapping using worm Ensemble IDs and the Associated Transcript Name<br/>
[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Mapping/wormbase.ensembl.idmapping wormbase_ensembl_idmapping ] ID mapping using Ensembl gene IDs and WormBase protein IDs<br/>
[http://archive.gersteinlab.org/proj/orthologs/Orthologs/Mapping/human.ensembl.idmapping human_ensembl_idmapping] ID mapping using human Ensemble IDs and the Associated Transcript Name<br/>

*Documentation<br/>
These are some powerpoints from previous presentation about the ortholog resources

[http://archive.gersteinlab.org/proj/orthologs/Orthologs/IDmapping.ppt ID_mapping.ppt]

* Contact People

Gang Fang, Rebecca Robilotto, Lincoln Stein, Mark Gerstein

Search

2011-02-17T16:06:26Z

Infoadmin:

* Searchable wiki of [http://wiki.gersteinlab.org/pubinfo Lab Information]

==FAQs==

* [http://faqs.gersteinlab.org/ FAQs]
* [http://bioinfo.mbb.yale.edu/pipermail/faq/ old FAQs]

==Search Engines==

Search

2011-02-17T15:57:39Z

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* [http://faqs.gersteinlab.org/ FAQs]
* [http://bioinfo.mbb.yale.edu/pipermail/faq/ old FAQs]
* [http://wiki.gersteinlab.org/pubinfo Lab Information]

Affiliated Organizations

2011-02-17T15:55:14Z

Infoadmin:

==Affiliated organizations within Yale==
* Compututational Biology & Bioinformatics Program ([http://ycmi.med.yale.edu/CBB/CBBProg.html CBB])
* [http://www.mbb.yale.edu MB&B] Department
* [http://www.cs.yale.edu CS] Department
* Center for Structural Biology ([http://www.csb.yale.edu CSB])
* Center for Genomics & Proteomics ([http://cgp.yale.edu CGP])
* Center for Excellence in Genome Sciences ([http://bioinfo.mbb.yale.edu/array CEGS])
* Yale Microarray Database ([http://www.med.yale.edu/microarray YMD]),
* NHLBI Proteomics [http://info.med.yale.edu/nhlbi-proteomics Center]

==Affiliated organizations beyond Yale==
* North East Structural Genomics Consortium ([http://www.nesg.org NESG.ORG]),
* [http://www.genome.gov/10005107 ENCODE] Consortium
* [http://www.modencode.org/ modENCODE] Consortium
* See also the [http://encode.gersteinlab.org Yale Encode Project]
* [http://www.1000genomes.org 1000 Genomes Consortium]

Affiliated Organizations

2011-02-17T15:54:35Z

Infoadmin:

==Affiliated organizations within Yale==
* Compututational Biology & Bioinformatics Program ([http://ycmi.med.yale.edu/CBB/CBBProg.html CBB])
* [http://www.mbb.yale.edu MB&B] Department
* [http://www.cs.yale.edu CS] Department
* Center for Structural Biology ([http://www.csb.yale.edu CSB])
* Center for Genomics & Proteomics ([http://cgp.yale.edu CGP])
* Center for Excellence in Genome Sciences ([http://bioinfo.mbb.yale.edu/array CEGS])
* Yale Microarray Database ([http://www.med.yale.edu/microarray YMD]),
* NHLBI Proteomics [http://info.med.yale.edu/nhlbi-proteomics Center]

==Affiliated organizations beyond Yale==
* North East Structural Genomics Consortium (<A HREF=http://www.nesg.org>NESG.ORG</A>),
* [http://www.genome.gov/10005107 ENCODE] Consortium
* [http://www.modencode.org/ modENCODE] Consortium
* See also the [http://encode.gersteinlab.org Yale Encode Project]
* [http://www.1000genomes.org 1000 Genomes Consortium]

Affiliated Organizations

2011-02-17T15:53:35Z

Infoadmin: Created page with '==Affiliated organizations within Yale== * Compututational Biology & Bioinformatics Program ([http://ycmi.med.yale.edu/CBB/CBBProg.html CBB]) * [http://www.mbb.yale.edu MB&B] Dep…'

==Affiliated organizations within Yale==
* Compututational Biology & Bioinformatics Program ([http://ycmi.med.yale.edu/CBB/CBBProg.html CBB])
* [http://www.mbb.yale.edu MB&B] Department
* [http://www.cs.yale.edu CS] Department
* Center for Structural Biology ([http://www.csb.yale.edu CSB])
* Center for Genomics & Proteomics ([http://cgp.yale.edu CGP])
* Center for Excellence in Genome Sciences ([http://bioinfo.mbb.yale.edu/array CEGS])
* Yale Microarray Database ([http://www.med.yale.edu/microarray YMD]),
* NHLBI Proteomics [http://info.med.yale.edu/nhlbi-proteomics Center]

==Affiliated organizations beyond Yale==
* North East Structural Genomics Consortium (<A HREF=http://www.nesg.org>NESG.ORG</A>),
* [http://www.genome.gov/10005107 ENCODE] Consortium
* [href="http://www.modencode.org/ modENCODE] Consortium
* See also [http://encode.gersteinlab.org Encode/Modencode Consortia]
* [http://www.1000genomes.org 1000 Genomes Consortium]

Calendar

2011-01-04T15:24:36Z

Infoadmin:

==Overview (Gerstein Lab Calendars and Listings of General Yale Bioinformatics Events)==
These two calendars are primarily for scheduling Gerstein Lab meetings, but include a number of special events and seminars that may be of general interest to the bioinformatics community at and around Yale. '''Gerstein Lab members should consult both calendars.''' If they are out-of-sync, please study them and related emails carefully and contact [http://contact.gerstein.info/ Mark] and the appropriate [[calendar maintainers]]. Other people should just contact [http://contact.gerstein.info/ Mark] for further information.

==Calendar #1 (Lab Events Curated by Lab Members)==
This calendar is [[calendar maintainers | collectively maintained by different people in the Gerstein Lab]] based on reading email lists and consulting Mark's calendar (below). Consult this for a curated and focused list of next week's events and call times. Information on subscribing to and updating this calendar is [http://wiki.gersteinlab.org/labinfo/Call_Calendar here]. ([http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com&ctz=America/New_York HTML] & [http://www.google.com/calendar/ical/gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com/public/basic.ics iCal])

{{#widget:Google Calendar
|id=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s@group.calendar.google.com
|title=GersteinLab Events curated by Lab members
|timezone=America/New_York
}}

==Calendar #2 (Lab PI's Calendar)==
Consult this for upcoming Yale seminars of interest and long term scheduling of group meetings and journal clubs (e.g. idays). Sometimes this is more slowly updated than #1.

([http://www.google.com/calendar/embed?title=GersteinLab+Events+from+MG+calendar&src=pleasepagemark%40gmail.com HTML] &
([http://www.google.com/calendar/ical/pleasepagemark%40gmail.com/private-ff6196e9fabae405a87bb6163f962bfb/basic.ics iCal])

{{#widget:Google Calendar
|id=pleasepagemark@gmail.com
|title=GersteinLab Events from MG calendar
|timezone=America/New_York
}}



==Description of Types of Events and Links to Other Calendars==
{| border="1"
! width=150 | TALK:
| width=550 | Those events marked "TALK" or "PUBLIC-TALK" are '''open to the public''' and recommended for those interested in bioinformatics. Make sure you click on the brief description for more details, often including an abstract. In connection with the pilot center in biomedical computing being developed at Yale, we are trying to present all the bioinformatics seminars in New Haven in an integrated fashion. As a first step, we have collected together many relevant seminars on this calendar.
|-
! *CBB*
| Those events marked "*CBB*" or "BCB-EVENT" are '''particular PUBLIC-TALKs that are strongly recommended to students in the [http://info.med.yale.edu/bbs/biocom.html CBB track].''' All track students should attend these, unless they have previously contacted the track directors about their absence beforehand.
|-
! OTHER-TALK:
| Similar to "TALK" but probably as not as directly relevant to bioinformatics.
|-
! TALK-IN-NY:
| This includes meetings of the [http://www.c2b2.columbia.edu/links/nycbs/nycbs.html New York Computational Biology Society] and public seminars of interest at NYC-area universities.
|-
! (Inf. Sem.)
| Will be advertised as an MB&B informal seminar.
|-
! LAB-ATTEND:
| '''All Gerstein group members are expected to attend events marked "LAB-ATTEND"''' or "ALL-ATTEND", unless they have discussed their absence beforehand. Usually these are group meetings (marked "gpmtg", see below) but sometimes they are particular public talks ("public-talk", see above). Careful attention is given to scheduling about one of these events per week. Mailings associated with these events will be sent to the group mailing list.
|-
! gpmtg
| For group meetings, the speaker in conjunction with Mark's assistant is responsible for reserving a room for events marked Bass424-or-TBA and notifying everyone of where the event will take place. The speaker is also responsible for reserving a laptop and the LCD. (Unless otherwise indicated group meetings are Gerstein-group only affairs.)
|-
! JC:
| Journal Club sessions cover subjects of general/particular interest to the lab and are optional except for members of the subgroup in parentheses, for whom attendance is compulsory. As for group meeting, the speaker is responsible for the venue and presentation medium.
|-
! TENT!
| Events marked "TENT!" are tentative and may be rescheduled.
|-
! SUBGRP
| Similar to "gpmtg" but applicable only to a subgroup.
|-
! OFFICE-HOUR:
| Denotes an office hour for M Gerstein, when he will be Bass 432, and not in other scheduled meetings. If these directly follow group meetings, the beginning time may be a bit loose, depending on the time the event ends.
|-
! OPT
| Optional events, such as [http://www.gersteinlab.org/frisbee frisbee] or [http://www.gersteinlab.org/squash squash]! (Frisbee is open to all. It is usually played on the lawn between Bass and Klein.)
|-
! *Y*
| Notifications from the [http://www.yale.edu/yalecollege/students/academics/calendar/index.html Yale College Calendar].
|}

Group meetings and journal clubs are usually in Bass 205, 305, or 405 or in Gibbs 362. Locations for events at Yale Med. School are at http://medicine.yale.edu/ysminfo/rooms/depart_rooms.html .

Collection of links relevant to seminars at Yale (try opening in tabs): [http://delicious.com/mbgmbg/placeyalecalendarquick Short and concise], [http://delicious.com/mbgmbg/placeyalecalendar Longer with redundancies]

CBB Calendar Page: http://cbb.yale.edu/calendars.html

==Old Calendars==
* Old calendar, used before Dec. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics2 http://calendar.yahoo.com/public/yalebioinformatics2])
** Some old information on keeping the above calendar updated (http://wiki.gersteinlab.org/labinfo/Calendar)
* Old calendar, used before Jan. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics http://calendar.yahoo.com/public/yalebioinformatics])
* Old calendar, used before Nov. 2004 ([http://calendar.yahoo.com/public/glpublic http://calendar.yahoo.com/public/glpublic])

Calendar

2010-12-30T12:09:07Z

Infoadmin: /* Calendar #2 (Lab PI's Calendar) */

==Overview (Gerstein Lab Calendars and Listings of General Yale Bioinformatics Events)==
These two calendars are primarily for scheduling Gerstein Lab meetings, but include a number of special events and seminars that may be of general interest to the bioinformatics community at and around Yale. '''Gerstein Lab members should consult both calendars.''' If they are out-of-sync, please study them and related emails carefully and contact [http://contact.gerstein.info/ Mark] and the appropriate [[calendar maintainers]]. Other people should just contact [http://contact.gerstein.info/ Mark] for further information.

==Calendar #1 (Lab Events Curated by Lab Members)==
This calendar is [[calendar maintainers | collectively maintained by different people in the Gerstein Lab]] based on reading email lists and consulting Mark's calendar (below). Consult this for a curated and focused list of next week's events and call times. Information on subscribing to and updating this calendar is [http://wiki.gersteinlab.org/labinfo/Call_Calendar here]. ([http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com&ctz=America/New_York HTML] & [http://www.google.com/calendar/ical/gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com/public/basic.ics iCal])

{{#widget:Google Calendar
|id=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s@group.calendar.google.com
|title=GersteinLab Events curated by Lab members
|timezone=America/New_York
}}

==Calendar #2 (Lab PI's Calendar)==
Consult this for upcoming Yale seminars of interest and long term scheduling of group meetings and journal clubs (e.g. idays). Sometimes this is more slowly updated than #1.

([http://www.google.com/calendar/embed?title=GersteinLab+Events+from+MG+calendar&src=pleasepagemark%40gmail.com HTML] &
([http://www.google.com/calendar/ical/pleasepagemark%40gmail.com/private-ff6196e9fabae405a87bb6163f962bfb/basic.ics iCal])

{{#widget:Google Calendar
|id=pleasepagemark@gmail.com
|title=GersteinLab Events from MG calendar
|timezone=America/New_York
}}

([http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=mark2%40gersteinlab.org&ctz=America/New_York HTML] & [http://www.google.com/calendar/ical/mark2%40gersteinlab.org/public/basic.ics iCal])

{{#widget:Google Calendar
|id=mark2@gersteinlab.org
|title=GersteinLab Events from MG calendar
|timezone=America/New_York
}}

==Description of Types of Events and Links to Other Calendars==
{| border="1"
! width=150 | TALK:
| width=550 | Those events marked "TALK" or "PUBLIC-TALK" are '''open to the public''' and recommended for those interested in bioinformatics. Make sure you click on the brief description for more details, often including an abstract. In connection with the pilot center in biomedical computing being developed at Yale, we are trying to present all the bioinformatics seminars in New Haven in an integrated fashion. As a first step, we have collected together many relevant seminars on this calendar.
|-
! *CBB*
| Those events marked "*CBB*" or "BCB-EVENT" are '''particular PUBLIC-TALKs that are strongly recommended to students in the [http://info.med.yale.edu/bbs/biocom.html CBB track].''' All track students should attend these, unless they have previously contacted the track directors about their absence beforehand.
|-
! OTHER-TALK:
| Similar to "TALK" but probably as not as directly relevant to bioinformatics.
|-
! TALK-IN-NY:
| This includes meetings of the [http://www.c2b2.columbia.edu/links/nycbs/nycbs.html New York Computational Biology Society] and public seminars of interest at NYC-area universities.
|-
! (Inf. Sem.)
| Will be advertised as an MB&B informal seminar.
|-
! LAB-ATTEND:
| '''All Gerstein group members are expected to attend events marked "LAB-ATTEND"''' or "ALL-ATTEND", unless they have discussed their absence beforehand. Usually these are group meetings (marked "gpmtg", see below) but sometimes they are particular public talks ("public-talk", see above). Careful attention is given to scheduling about one of these events per week. Mailings associated with these events will be sent to the group mailing list.
|-
! gpmtg
| For group meetings, the speaker in conjunction with Mark's assistant is responsible for reserving a room for events marked Bass424-or-TBA and notifying everyone of where the event will take place. The speaker is also responsible for reserving a laptop and the LCD. (Unless otherwise indicated group meetings are Gerstein-group only affairs.)
|-
! JC:
| Journal Club sessions cover subjects of general/particular interest to the lab and are optional except for members of the subgroup in parentheses, for whom attendance is compulsory. As for group meeting, the speaker is responsible for the venue and presentation medium.
|-
! TENT!
| Events marked "TENT!" are tentative and may be rescheduled.
|-
! SUBGRP
| Similar to "gpmtg" but applicable only to a subgroup.
|-
! OFFICE-HOUR:
| Denotes an office hour for M Gerstein, when he will be Bass 432, and not in other scheduled meetings. If these directly follow group meetings, the beginning time may be a bit loose, depending on the time the event ends.
|-
! OPT
| Optional events, such as [http://www.gersteinlab.org/frisbee frisbee] or [http://www.gersteinlab.org/squash squash]! (Frisbee is open to all. It is usually played on the lawn between Bass and Klein.)
|-
! *Y*
| Notifications from the [http://www.yale.edu/yalecollege/students/academics/calendar/index.html Yale College Calendar].
|}

Group meetings and journal clubs are usually in Bass 205, 305, or 405 or in Gibbs 362. Locations for events at Yale Med. School are at http://medicine.yale.edu/ysminfo/rooms/depart_rooms.html .

Collection of links relevant to seminars at Yale (try opening in tabs): [http://delicious.com/mbgmbg/placeyalecalendarquick Short and concise], [http://delicious.com/mbgmbg/placeyalecalendar Longer with redundancies]

CBB Calendar Page: http://cbb.yale.edu/calendars.html

==Old Calendars==
* Old calendar, used before Dec. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics2 http://calendar.yahoo.com/public/yalebioinformatics2])
** Some old information on keeping the above calendar updated (http://wiki.gersteinlab.org/labinfo/Calendar)
* Old calendar, used before Jan. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics http://calendar.yahoo.com/public/yalebioinformatics])
* Old calendar, used before Nov. 2004 ([http://calendar.yahoo.com/public/glpublic http://calendar.yahoo.com/public/glpublic])

Calendar

2010-12-30T12:08:29Z

Infoadmin:

==Overview (Gerstein Lab Calendars and Listings of General Yale Bioinformatics Events)==
These two calendars are primarily for scheduling Gerstein Lab meetings, but include a number of special events and seminars that may be of general interest to the bioinformatics community at and around Yale. '''Gerstein Lab members should consult both calendars.''' If they are out-of-sync, please study them and related emails carefully and contact [http://contact.gerstein.info/ Mark] and the appropriate [[calendar maintainers]]. Other people should just contact [http://contact.gerstein.info/ Mark] for further information.

==Calendar #1 (Lab Events Curated by Lab Members)==
This calendar is [[calendar maintainers | collectively maintained by different people in the Gerstein Lab]] based on reading email lists and consulting Mark's calendar (below). Consult this for a curated and focused list of next week's events and call times. Information on subscribing to and updating this calendar is [http://wiki.gersteinlab.org/labinfo/Call_Calendar here]. ([http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com&ctz=America/New_York HTML] & [http://www.google.com/calendar/ical/gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com/public/basic.ics iCal])

{{#widget:Google Calendar
|id=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s@group.calendar.google.com
|title=GersteinLab Events curated by Lab members
|timezone=America/New_York
}}

==Calendar #2 (Lab PI's Calendar)==
Consult this for upcoming Yale seminars of interest and long term scheduling of group meetings and journal clubs (e.g. idays). Sometimes this is more slowly updated than #1.

([https://www.google.com/calendar/embed?title=GersteinLab+Events+from+MG+calendar&src=pleasepagemark%40gmail.com] &
([http://www.google.com/calendar/ical/pleasepagemark%40gmail.com/private-ff6196e9fabae405a87bb6163f962bfb/basic.ics iCal])

{{#widget:Google Calendar
|id=pleasepagemark@gmail.com
|title=GersteinLab Events from MG calendar
|timezone=America/New_York
}}

([http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=mark2%40gersteinlab.org&ctz=America/New_York HTML] & [http://www.google.com/calendar/ical/mark2%40gersteinlab.org/public/basic.ics iCal])

{{#widget:Google Calendar
|id=mark2@gersteinlab.org
|title=GersteinLab Events from MG calendar
|timezone=America/New_York
}}

==Description of Types of Events and Links to Other Calendars==
{| border="1"
! width=150 | TALK:
| width=550 | Those events marked "TALK" or "PUBLIC-TALK" are '''open to the public''' and recommended for those interested in bioinformatics. Make sure you click on the brief description for more details, often including an abstract. In connection with the pilot center in biomedical computing being developed at Yale, we are trying to present all the bioinformatics seminars in New Haven in an integrated fashion. As a first step, we have collected together many relevant seminars on this calendar.
|-
! *CBB*
| Those events marked "*CBB*" or "BCB-EVENT" are '''particular PUBLIC-TALKs that are strongly recommended to students in the [http://info.med.yale.edu/bbs/biocom.html CBB track].''' All track students should attend these, unless they have previously contacted the track directors about their absence beforehand.
|-
! OTHER-TALK:
| Similar to "TALK" but probably as not as directly relevant to bioinformatics.
|-
! TALK-IN-NY:
| This includes meetings of the [http://www.c2b2.columbia.edu/links/nycbs/nycbs.html New York Computational Biology Society] and public seminars of interest at NYC-area universities.
|-
! (Inf. Sem.)
| Will be advertised as an MB&B informal seminar.
|-
! LAB-ATTEND:
| '''All Gerstein group members are expected to attend events marked "LAB-ATTEND"''' or "ALL-ATTEND", unless they have discussed their absence beforehand. Usually these are group meetings (marked "gpmtg", see below) but sometimes they are particular public talks ("public-talk", see above). Careful attention is given to scheduling about one of these events per week. Mailings associated with these events will be sent to the group mailing list.
|-
! gpmtg
| For group meetings, the speaker in conjunction with Mark's assistant is responsible for reserving a room for events marked Bass424-or-TBA and notifying everyone of where the event will take place. The speaker is also responsible for reserving a laptop and the LCD. (Unless otherwise indicated group meetings are Gerstein-group only affairs.)
|-
! JC:
| Journal Club sessions cover subjects of general/particular interest to the lab and are optional except for members of the subgroup in parentheses, for whom attendance is compulsory. As for group meeting, the speaker is responsible for the venue and presentation medium.
|-
! TENT!
| Events marked "TENT!" are tentative and may be rescheduled.
|-
! SUBGRP
| Similar to "gpmtg" but applicable only to a subgroup.
|-
! OFFICE-HOUR:
| Denotes an office hour for M Gerstein, when he will be Bass 432, and not in other scheduled meetings. If these directly follow group meetings, the beginning time may be a bit loose, depending on the time the event ends.
|-
! OPT
| Optional events, such as [http://www.gersteinlab.org/frisbee frisbee] or [http://www.gersteinlab.org/squash squash]! (Frisbee is open to all. It is usually played on the lawn between Bass and Klein.)
|-
! *Y*
| Notifications from the [http://www.yale.edu/yalecollege/students/academics/calendar/index.html Yale College Calendar].
|}

Group meetings and journal clubs are usually in Bass 205, 305, or 405 or in Gibbs 362. Locations for events at Yale Med. School are at http://medicine.yale.edu/ysminfo/rooms/depart_rooms.html .

Collection of links relevant to seminars at Yale (try opening in tabs): [http://delicious.com/mbgmbg/placeyalecalendarquick Short and concise], [http://delicious.com/mbgmbg/placeyalecalendar Longer with redundancies]

CBB Calendar Page: http://cbb.yale.edu/calendars.html

==Old Calendars==
* Old calendar, used before Dec. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics2 http://calendar.yahoo.com/public/yalebioinformatics2])
** Some old information on keeping the above calendar updated (http://wiki.gersteinlab.org/labinfo/Calendar)
* Old calendar, used before Jan. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics http://calendar.yahoo.com/public/yalebioinformatics])
* Old calendar, used before Nov. 2004 ([http://calendar.yahoo.com/public/glpublic http://calendar.yahoo.com/public/glpublic])

Calendar

2010-12-30T12:03:35Z

Infoadmin:

==Overview (Gerstein Lab Calendars and Listings of General Yale Bioinformatics Events)==
These two calendars are primarily for scheduling Gerstein Lab meetings, but include a number of special events and seminars that may be of general interest to the bioinformatics community at and around Yale. '''Gerstein Lab members should consult both calendars.''' If they are out-of-sync, please study them and related emails carefully and contact [http://contact.gerstein.info/ Mark] and the appropriate [[calendar maintainers]]. Other people should just contact [http://contact.gerstein.info/ Mark] for further information.

==Calendar #1 (Lab Events Curated by Lab Members)==
This calendar is [[calendar maintainers | collectively maintained by different people in the Gerstein Lab]] based on reading email lists and consulting Mark's calendar (below). Consult this for a curated and focused list of next week's events and call times. Information on subscribing to and updating this calendar is [http://wiki.gersteinlab.org/labinfo/Call_Calendar here]. ([http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com&ctz=America/New_York HTML] & [http://www.google.com/calendar/ical/gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s%40group.calendar.google.com/public/basic.ics iCal])

{{#widget:Google Calendar
|id=gersteinlab.org_j6svgs6fpgmiqni0pnqepr062s@group.calendar.google.com
|title=GersteinLab Events curated by Lab members
|timezone=America/New_York
}}

==Calendar #2 (Lab PI's Calendar)==
Consult this for upcoming Yale seminars of interest and long term scheduling of group meetings and journal clubs (e.g. idays). Sometimes this is more slowly updated than #1.

([http://www.google.com/calendar/ical/pleasepagemark%40gmail.com/private-ff6196e9fabae405a87bb6163f962bfb/basic.ics iCal])

{{#widget:Google Calendar
|id=pleasepagemark@gmail.com
|title=GersteinLab Events from MG calendar
|timezone=America/New_York
}}

([http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=mark2%40gersteinlab.org&ctz=America/New_York HTML] & [http://www.google.com/calendar/ical/mark2%40gersteinlab.org/public/basic.ics iCal])

{{#widget:Google Calendar
|id=mark2@gersteinlab.org
|title=GersteinLab Events from MG calendar
|timezone=America/New_York
}}

==Description of Types of Events and Links to Other Calendars==
{| border="1"
! width=150 | TALK:
| width=550 | Those events marked "TALK" or "PUBLIC-TALK" are '''open to the public''' and recommended for those interested in bioinformatics. Make sure you click on the brief description for more details, often including an abstract. In connection with the pilot center in biomedical computing being developed at Yale, we are trying to present all the bioinformatics seminars in New Haven in an integrated fashion. As a first step, we have collected together many relevant seminars on this calendar.
|-
! *CBB*
| Those events marked "*CBB*" or "BCB-EVENT" are '''particular PUBLIC-TALKs that are strongly recommended to students in the [http://info.med.yale.edu/bbs/biocom.html CBB track].''' All track students should attend these, unless they have previously contacted the track directors about their absence beforehand.
|-
! OTHER-TALK:
| Similar to "TALK" but probably as not as directly relevant to bioinformatics.
|-
! TALK-IN-NY:
| This includes meetings of the [http://www.c2b2.columbia.edu/links/nycbs/nycbs.html New York Computational Biology Society] and public seminars of interest at NYC-area universities.
|-
! (Inf. Sem.)
| Will be advertised as an MB&B informal seminar.
|-
! LAB-ATTEND:
| '''All Gerstein group members are expected to attend events marked "LAB-ATTEND"''' or "ALL-ATTEND", unless they have discussed their absence beforehand. Usually these are group meetings (marked "gpmtg", see below) but sometimes they are particular public talks ("public-talk", see above). Careful attention is given to scheduling about one of these events per week. Mailings associated with these events will be sent to the group mailing list.
|-
! gpmtg
| For group meetings, the speaker in conjunction with Mark's assistant is responsible for reserving a room for events marked Bass424-or-TBA and notifying everyone of where the event will take place. The speaker is also responsible for reserving a laptop and the LCD. (Unless otherwise indicated group meetings are Gerstein-group only affairs.)
|-
! JC:
| Journal Club sessions cover subjects of general/particular interest to the lab and are optional except for members of the subgroup in parentheses, for whom attendance is compulsory. As for group meeting, the speaker is responsible for the venue and presentation medium.
|-
! TENT!
| Events marked "TENT!" are tentative and may be rescheduled.
|-
! SUBGRP
| Similar to "gpmtg" but applicable only to a subgroup.
|-
! OFFICE-HOUR:
| Denotes an office hour for M Gerstein, when he will be Bass 432, and not in other scheduled meetings. If these directly follow group meetings, the beginning time may be a bit loose, depending on the time the event ends.
|-
! OPT
| Optional events, such as [http://www.gersteinlab.org/frisbee frisbee] or [http://www.gersteinlab.org/squash squash]! (Frisbee is open to all. It is usually played on the lawn between Bass and Klein.)
|-
! *Y*
| Notifications from the [http://www.yale.edu/yalecollege/students/academics/calendar/index.html Yale College Calendar].
|}

Group meetings and journal clubs are usually in Bass 205, 305, or 405 or in Gibbs 362. Locations for events at Yale Med. School are at http://medicine.yale.edu/ysminfo/rooms/depart_rooms.html .

Collection of links relevant to seminars at Yale (try opening in tabs): [http://delicious.com/mbgmbg/placeyalecalendarquick Short and concise], [http://delicious.com/mbgmbg/placeyalecalendar Longer with redundancies]

CBB Calendar Page: http://cbb.yale.edu/calendars.html

==Old Calendars==
* Old calendar, used before Dec. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics2 http://calendar.yahoo.com/public/yalebioinformatics2])
** Some old information on keeping the above calendar updated (http://wiki.gersteinlab.org/labinfo/Calendar)
* Old calendar, used before Jan. 2008 ([http://calendar.yahoo.com/public/yalebioinformatics http://calendar.yahoo.com/public/yalebioinformatics])
* Old calendar, used before Nov. 2004 ([http://calendar.yahoo.com/public/glpublic http://calendar.yahoo.com/public/glpublic])

Pi at gersteinlab.org

2010-12-10T08:17:43Z

Infoadmin:

Pi at gersteinlab.org

2010-12-10T08:09:01Z

Infoadmin:

Pi at gersteinlab.org

2010-12-10T08:07:26Z

Infoadmin: Created page with '* Use pi at gersteinlab.org address for paper correspondence. ** Contact the lab manager for access to the pi2 at gersteinlab.org account ** The lab manager (currently MF) will …'

Xxmg at gersteinlab.org

2010-12-10T08:03:22Z

Infoadmin:

'''The instructions in this page is DEPRECATED'''

The correct address to use is [[pi at gersteinlab.org]]

----

* '''xx'''mg@gersteinlab.org address for paper correspondence.
** Try to use '''xx'''mg@gersteinlab.org, where '''xx''' is your lab initials . For instance, hymg (at) gersteinlab.org, would be the corresponding address for Haiyuan Yu. This address should be set to fork to xx and MG and used for all correspondence. This should be the corresponding author address and should be signed as MG -- i.e. "Mark Gerstein" <xxmg@gersteinlab.org>. The idea behind this is to list MG as the corresponding author but allow the lab member to receive all correspondence and respond to this as MG.
** Make sure you sign all of these emails as Mark Gerstein (not as yourself!).
** The xxmg@gersteinlab.org email address should be changed to Mark.Gerstein at Yale.edu (see http://contact.gerstein.info) at the very end at the proof stage.
** Note that you can trivially change gmail, Yahoo mail or firefox to allow you to email '''from''' xxmg@gersteinlab.org . (For gmail, make sure you go through Yale servers and authenticate properly so you don't have a different sender.)
** When you send something from this address BCC or CC back to xxmg@gersteinlab.org. Do '''not''' CC it to your or Mark's normal email address as this only confuses things.
** The lab manager (currently MF) will configure these addresses on demand.

Xxmg at gersteinlab.org

2010-12-10T08:02:54Z

Infoadmin:

'''The instructions in this page is DEPRECATED'''

The correct address to use is [pi at gersteinlab.org]

----

* '''xx'''mg@gersteinlab.org address for paper correspondence.
** Try to use '''xx'''mg@gersteinlab.org, where '''xx''' is your lab initials . For instance, hymg (at) gersteinlab.org, would be the corresponding address for Haiyuan Yu. This address should be set to fork to xx and MG and used for all correspondence. This should be the corresponding author address and should be signed as MG -- i.e. "Mark Gerstein" <xxmg@gersteinlab.org>. The idea behind this is to list MG as the corresponding author but allow the lab member to receive all correspondence and respond to this as MG.
** Make sure you sign all of these emails as Mark Gerstein (not as yourself!).
** The xxmg@gersteinlab.org email address should be changed to Mark.Gerstein at Yale.edu (see http://contact.gerstein.info) at the very end at the proof stage.
** Note that you can trivially change gmail, Yahoo mail or firefox to allow you to email '''from''' xxmg@gersteinlab.org . (For gmail, make sure you go through Yale servers and authenticate properly so you don't have a different sender.)
** When you send something from this address BCC or CC back to xxmg@gersteinlab.org. Do '''not''' CC it to your or Mark's normal email address as this only confuses things.
** The lab manager (currently MF) will configure these addresses on demand.