GersteinInfo - User contributions [en]

Main Page

2011-06-08T23:22:58Z

Rar62:

This wiki hosts general, public information about the

'''[http://gersteinlab.org Gerstein Lab]'''.

Lab members should consult the [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "private"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

== Important Public Items ==
*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
* 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])

== 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://araman.mbgnet/nagios/ System Status] MBGNet LAN access only.
* [http://info.gersteinlab.org/Tools Tools] page

Tools

2011-06-02T02:29:25Z

Rar62:

[http://molmovdb.org/molmovdb/morph Morph Server] generates a plausible pathway between two conformations of a protein or nucleic acid structure. A large number of statistics and several high-quality movies are output.

[http://bioinfo.mbb.yale.edu/ExpressYourself ExpressYourself] is an interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.

[http://spine.nesg.org SPINE] is our laboratory-information management system (LIMS) for the [http://www.nesg.org NorthEast Structural Genomics Consortium]. The online version is restricted to consortium users, but most of the code is freely available for download.<br>

[http://pseudogene.org Pseudogene.org] is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several
organisms.

[http://tiling.gersteinlab.org Tiling] is under construction.

[http://networks.gersteinlab.org/genome/interactions/networks/ TopNet] is an automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.

A number of programs for calculating properties of protein and nucleic
acid structures have been collected into a [http://geometry.molmovdb.org single distribution]. Included are a library of utility functions for dealing
with structures, and a convenient interactive command-line interpreter.

A new algorithm for [http://bioinfo.mbb.yale.edu/expression/cluster local clustering of expression data] to find timeshifted and/or inverted
relationships is available as C source code.

Tools

2011-06-02T02:27:12Z

Rar62:

[http://molmovdb.org/molmovdb/morph Morph Server] generates a plausible pathway between two conformations of a protein or nucleic acid structure. A large number of statistics and several high-quality movies are output.
<SMALL>[ <A HREF="/papers/morphs-nar">citation 1</A> | <A
HREF="/papers/molmovdb2">citation2</A> |
<A HREf="/papers/subject/motions">related</A> ]</SMALL>

[http://bioinfo.mbb.yale.edu/ExpressYourself ExpressYourself] is an interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
<SMALL>[ <A HREf="/papers/expressyourself">citation</A> ]</SMALL>

[http://spine.nesg.org SPINE] is our laboratory-information management system (LIMS) for the [http://www.nesg.org NorthEast Structural Genomics Consortium]. The online version is restricted to consortium users, but most of the code is freely available for download.<br>

<SMALL>[ <A HREF="/papers/spine-nar">citation1</A> | <A
HREF="/papers/spine2-nar">citation2</A> ]</SMALL>

[http://pseudogene.org Pseudogene.org] is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several
organisms.

[http://tiling.gersteinlab.org Tiling] is under construction.

[http://networks.gersteinlab.org/genome/interactions/networks/ TopNet] is an automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.

A number of programs for calculating properties of protein and nucleic
acid structures have been collected into a [http://geometry.molmovdb.org single distribution]. Included are a library of utility functions for dealing
with structures, and a convenient interactive command-line interpreter.
<SMALL>[ <A HREF="/papers/subject/volumes">related papers</A> ]</SMALL>

A new algorithm for [http://bioinfo.mbb.yale.edu/expression/cluster local clustering of expression data] to find timeshifted and/or inverted
relationships is available as C source code.
<SMALL>[ <A HREF="/papers/timeshift-jmb">citation</A> ]</SMALL>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="/papers/xml/">
<IMG SRC="./images/papers.png" ALT="Papers"></A>
</TD>
<TD CLASS="description">
The <A CLASS="resource" HREF="/papers">publication listings</A> on our
site are automatically
generated based on data from the NCBI and local annotations stored in XML
format. The <A CLASS="resource" HREF="/papers/xml">code</A> which does
this is freely available
(some modification will be required for other sites).

</TD>
</TR>
</HTML>

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

Main Page

2011-06-02T02:12:09Z

Rar62: /* Info for Lab Members and Collaborators */

This wiki hosts general, public information about the [http://gersteinlab.org Gerstein Lab]. Lab members should consult the [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "private"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

== Important Public Items ==
*Public [[Documents]] about the lab
*[[FAQ]] (new) on programs
*Prominent [[public wiki pages linked from elsewhere]]

== Info for New People ==
*[[General Information for New Undergraduates]] thinking about working in the lab
* 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])

== 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://araman.mbgnet/nagios/ System Status] MBGNet LAN access only.
* [http://info.gersteinlab.org/Tools Tools] page

Tools

2011-06-01T22:12:08Z

Rar62:

<HTML>

<TABLE CELLPADDING="0">
<TR>

<TD CLASS="bg">
<TABLE CELLPADDING="8" CELLSPACING="1">
<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://molmovdb.org/molmovdb/morph">
<IMG SRC="./images/morph-icon.jpg" ALT="Morph Server"></A>
</TD>
<TD CLASS="description">
The <A CLASS="resource"
HREF="http://molmovdb.org/molmovdb/morph">Morph Server</A>
generates
a plausible pathway between two conformations of a protein or nucleic acid
structure.
A large number of statistics and several high-quality movies are
output.<br>
<SMALL>[ <A HREF="/papers/morphs-nar">citation 1</A> | <A
HREF="/papers/molmovdb2">citation2</A> |
<A HREf="/papers/subject/motions">related</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://bioinfo.mbb.yale.edu/ExpressYourself">
<IMG SRC="./images/express-logo.png" ALT="ExpressYourself"></A>
</TD>
<TD CLASS="description">
<A CLASS="resource" HREF="http://bioinfo.mbb.yale.edu/ExpressYourself">ExpressYourself</A> is an
interactive platform for
background correction, normalization, scoring, and quality assessment of
raw microarray data.<br>
<SMALL>[ <A HREf="/papers/expressyourself">citation</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://spine.nesg.org">
<IMG SRC="./images/spine-icon.jpg" ALT="SPINE"></A>
</TD>
<TD CLASS="description">
<A CLASS="resource" HREF="http://spine.nesg.org">SPINE</A> is our
laboratory-information management
system (LIMS) for the <A CLASS="resource"
HREf="http://www.nesg.org">NorthEast Structural Genomics
Consortium</A>. The online version is restricted to consortium users, but
most of the code is
freely available for download.<br>

<SMALL>[ <A HREF="/papers/spine-nar">citation1</A> | <A
HREF="/papers/spine2-nar">citation2</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://pseudogene.org">
<IMG SRC="./images/pseudogene.png" ALT="Pseudogenes"></A>
</TD>

<TD CLASS="description">
<a class="resource" href="http://pseudogene.org">Pseudogene.org</a>
is a collection of resources related to our efforts to survey
eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage,
amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help
elucidate the relationships between pseudogene families across several
organisms.
</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://tiling.gersteinlab.org/">
<IMG SRC="./images/tiling.png" ALT="Tiling"></A>
</TD>
<TD CLASS="description">
<a class="resource" href="http://tiling.gersteinlab.org/">Tiling</a>
is under construction.
</TD>

</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://networks.gersteinlab.org/genome/interactions/networks/">
<IMG SRC="./images/topnet.png" ALT="TopNet"></A>
</TD>
<TD CLASS="description">
<a class="resource" href="http://networks.gersteinlab.org/genome/interactions/networks/">TopNet</a>
is an automated web tool designed to calculate topological
parameters and compare different sub-networks for any given network.
</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://geometry.molmovdb.org">

<IMG SRC="./images/volume.png" ALT="Protein Geometry"></A>
</TD>
<TD CLASS="description">
A number of programs for calculating properties of protein and nucleic
acid structures have
been collected into a <A CLASS="resource"
HREF="http://geometry.molmovdb.org">single
distribution</A>. Included are a library of utility functions for dealing
with structures,
and a convenient interactive command-line interpreter.
<SMALL>[ <A HREF="/papers/subject/volumes">related papers</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">

<A CLASS="image" HREF="http://bioinfo.mbb.yale.edu/expression/cluster">
<IMG SRC="./images/timeshift.png" ALT="Local Clustering"></A>
</TD>
<TD CLASS="description">
A new algorithm for <A CLASS="resource" HREF="http://bioinfo.mbb.yale.edu/expression/cluster">local
clustering of expression data</A> to find timeshifted and/or inverted
relationships is available as C source code.
<SMALL>[ <A HREF="/papers/timeshift-jmb">citation</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="/papers/xml/">
<IMG SRC="./images/papers.png" ALT="Papers"></A>
</TD>
<TD CLASS="description">
The <A CLASS="resource" HREF="/papers">publication listings</A> on our
site are automatically
generated based on data from the NCBI and local annotations stored in XML
format. The <A CLASS="resource" HREF="/papers/xml">code</A> which does
this is freely available
(some modification will be required for other sites).

</TD>
</TR>
</HTML>

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

Tools

2011-06-01T22:11:42Z

Rar62: Created page with '<TABLE CELLPADDING="0"> <TR> <TD CLASS="bg"> <TABLE CELLPADDING="8" CELLSPACING="1"> <TR> <TD CLASS="image" VALIGN="middle"> <A CLASS="image" HREF="http://molmovdb.org/molmovdb/…'

<TABLE CELLPADDING="0">
<TR>

<TD CLASS="bg">
<TABLE CELLPADDING="8" CELLSPACING="1">
<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://molmovdb.org/molmovdb/morph">
<IMG SRC="./images/morph-icon.jpg" ALT="Morph Server"></A>
</TD>
<TD CLASS="description">
The <A CLASS="resource"
HREF="http://molmovdb.org/molmovdb/morph">Morph Server</A>
generates
a plausible pathway between two conformations of a protein or nucleic acid
structure.
A large number of statistics and several high-quality movies are
output.<br>
<SMALL>[ <A HREF="/papers/morphs-nar">citation 1</A> | <A
HREF="/papers/molmovdb2">citation2</A> |
<A HREf="/papers/subject/motions">related</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://bioinfo.mbb.yale.edu/ExpressYourself">
<IMG SRC="./images/express-logo.png" ALT="ExpressYourself"></A>
</TD>
<TD CLASS="description">
<A CLASS="resource" HREF="http://bioinfo.mbb.yale.edu/ExpressYourself">ExpressYourself</A> is an
interactive platform for
background correction, normalization, scoring, and quality assessment of
raw microarray data.<br>
<SMALL>[ <A HREf="/papers/expressyourself">citation</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://spine.nesg.org">
<IMG SRC="./images/spine-icon.jpg" ALT="SPINE"></A>
</TD>
<TD CLASS="description">
<A CLASS="resource" HREF="http://spine.nesg.org">SPINE</A> is our
laboratory-information management
system (LIMS) for the <A CLASS="resource"
HREf="http://www.nesg.org">NorthEast Structural Genomics
Consortium</A>. The online version is restricted to consortium users, but
most of the code is
freely available for download.<br>

<SMALL>[ <A HREF="/papers/spine-nar">citation1</A> | <A
HREF="/papers/spine2-nar">citation2</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://pseudogene.org">
<IMG SRC="./images/pseudogene.png" ALT="Pseudogenes"></A>
</TD>

<TD CLASS="description">
<a class="resource" href="http://pseudogene.org">Pseudogene.org</a>
is a collection of resources related to our efforts to survey
eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage,
amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help
elucidate the relationships between pseudogene families across several
organisms.
</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://tiling.gersteinlab.org/">
<IMG SRC="./images/tiling.png" ALT="Tiling"></A>
</TD>
<TD CLASS="description">
<a class="resource" href="http://tiling.gersteinlab.org/">Tiling</a>
is under construction.
</TD>

</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://networks.gersteinlab.org/genome/interactions/networks/">
<IMG SRC="./images/topnet.png" ALT="TopNet"></A>
</TD>
<TD CLASS="description">
<a class="resource" href="http://networks.gersteinlab.org/genome/interactions/networks/">TopNet</a>
is an automated web tool designed to calculate topological
parameters and compare different sub-networks for any given network.
</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="http://geometry.molmovdb.org">

<IMG SRC="./images/volume.png" ALT="Protein Geometry"></A>
</TD>
<TD CLASS="description">
A number of programs for calculating properties of protein and nucleic
acid structures have
been collected into a <A CLASS="resource"
HREF="http://geometry.molmovdb.org">single
distribution</A>. Included are a library of utility functions for dealing
with structures,
and a convenient interactive command-line interpreter.
<SMALL>[ <A HREF="/papers/subject/volumes">related papers</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">

<A CLASS="image" HREF="http://bioinfo.mbb.yale.edu/expression/cluster">
<IMG SRC="./images/timeshift.png" ALT="Local Clustering"></A>
</TD>
<TD CLASS="description">
A new algorithm for <A CLASS="resource" HREF="http://bioinfo.mbb.yale.edu/expression/cluster">local
clustering of expression data</A> to find timeshifted and/or inverted
relationships is available as C source code.
<SMALL>[ <A HREF="/papers/timeshift-jmb">citation</A> ]</SMALL>

</TD>
</TR>

<TR>
<TD CLASS="image" VALIGN="middle">
<A CLASS="image" HREF="/papers/xml/">
<IMG SRC="./images/papers.png" ALT="Papers"></A>
</TD>
<TD CLASS="description">
The <A CLASS="resource" HREF="/papers">publication listings</A> on our
site are automatically
generated based on data from the NCBI and local annotations stored in XML
format. The <A CLASS="resource" HREF="/papers/xml">code</A> which does
this is freely available
(some modification will be required for other sites).

</TD>
</TR>

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

Main Page

2011-05-31T16:14:48Z

Rar62: /* Info for Lab Members and Collaborators */