http://bioinfo-core.org/api.php?action=feedcontributions&user=Rebhan&feedformat=atomBioWiki - User contributions [en]2024-03-28T13:13:58ZUser contributionsMediaWiki 1.34.0http://bioinfo-core.org/index.php?title=Category:Meetings&diff=4084Category:Meetings2008-10-11T10:05:08Z<p>Rebhan: New page: Meetings related to bioinformatics cores, including our conference calls, bioinformatics conferences etc.</p>
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<div>Meetings related to bioinformatics cores, including our conference calls, bioinformatics conferences etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=Call_Minutes&diff=4083Call Minutes2008-10-11T10:03:36Z<p>Rebhan: </p>
<hr />
<div>[[Category:Meetings]]<br />
<br />
On a rough quarterly basis, bioinfo-core members participate in discussions of topical interest. These occur either through a conference call or during BoF sessions at the annual ISMB conference.<br />
<br />
Please find below minutes and/or slide presentations from the quarterly meetings.<br />
<br />
Minutes<br />
* [[15 October 2007]]: '''Solexa Sequencing from ILMN's pipeline to Infrastructure requirements.'''<br />
* [[4 February 2008]]: '''Education for Biologists; Tools utilized by Biologists and Cores.'''<br />
* [[8 May 2008]]: '''BoF's at ISMB 08 Call for presentations; Handling ePHI, and Cloud/SaaS related ePHI.'''<br />
* [[20 July 2008]]: '''ISMB2008 BoF: Next-Generation Sequencing: Practical Aspects of Running a Core'''<br />
* [[22 July 2008]]: '''ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility'''</div>Rebhanhttp://bioinfo-core.org/index.php?title=Main_Page&diff=4082Main Page2008-10-11T10:02:50Z<p>Rebhan: </p>
<hr />
<div>'''Welcome to the bioinfo-core's wiki!''' <br />
<br />
== Introduction ==<br />
<br />
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. Through this wiki and our online [http://lists.open-bio.org/mailman/listinfo/bioinfo-core discussion lists] we discuss many topics that are challenging bioinformatics cores world wide. From IT, new instrumentation, staffing and training bioinformaticians, tools, software, to services for biologists and MD's.<br />
<BR><BR><br />
We hold several events throughout the year including quarterly conference calls (with published [[Call Minutes]]) and a yearly set of informal presentations and dinners at the annual meeting, Intelligent Systems in Molecular Biology ([http://www.iscb.org/conf_edu.shtml ISMB]), the official conference of [http://www.iscb.org/ ISCB]<br />
<br><br><br />
Please browse, add and participate in the wiki and the discussion lists. To edit the wiki, create a New Account and then edit the [[BioWiki:Community Portal]] to add a link for your core facility and its description.<br />
<br />
== Wiki page links ==<br />
*[[Call Minutes]]: Detailed minutes from quarterly conference calls on selected and pertinent topics, and annual meetings complete with presenations<br />
*[[BioWiki:Community Portal]]: list your organization!<br />
*[[Ongoing Discussions]]: discussion forums including lists of software, tools, etc.<br />
*[[Special:Categories]]: find pages using categories such as Tools, Presentations, NextGenSequencing, Meetings etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=Main_Page&diff=4081Main Page2008-10-11T09:57:08Z<p>Rebhan: /* Wiki page links */</p>
<hr />
<div>'''Welcome to the bioinfo-core's wiki!''' <br />
<br />
== Introduction ==<br />
<br />
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. Through this wiki and our online [http://lists.open-bio.org/mailman/listinfo/bioinfo-core discussion lists] we discuss many topics that are challenging bioinformatics cores world wide. From IT, new instrumentation, staffing and training bioinformaticians, tools, software, to services for biologists and MD's.<br />
<BR><BR><br />
We hold several events throughout the year including quarterly conference calls (with published [[Call Minutes]]) and a yearly set of informal presentations and dinners at the annual meeting, Intelligent Systems in Molecular Biology ([http://www.iscb.org/conf_edu.shtml ISMB]), the official conference of [http://www.iscb.org/ ISCB]<br />
<br><br><br />
Please browse, add and participate in the wiki and the discussion lists. To edit the wiki, create a New Account and then edit the [[BioWiki:Community Portal]] to add a link for your core facility and its description.<br />
<br />
== Wiki page links ==<br />
*[[Call Minutes]]: Detailed minutes from quarterly conference calls on selected and pertinent topics, and annual meetings complete with presenations<br />
*[[BioWiki:Community Portal]]: list your organization!<br />
*[[Ongoing Discussions]]: discussion forums including lists of software, tools, etc.<br />
*[[Special:Categories]]: find pages using categories such as Tools, Presentations, NextGenSequencing etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=Main_Page&diff=4080Main Page2008-10-11T09:56:20Z<p>Rebhan: </p>
<hr />
<div>'''Welcome to the bioinfo-core's wiki!''' <br />
<br />
== Introduction ==<br />
<br />
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. Through this wiki and our online [http://lists.open-bio.org/mailman/listinfo/bioinfo-core discussion lists] we discuss many topics that are challenging bioinformatics cores world wide. From IT, new instrumentation, staffing and training bioinformaticians, tools, software, to services for biologists and MD's.<br />
<BR><BR><br />
We hold several events throughout the year including quarterly conference calls (with published [[Call Minutes]]) and a yearly set of informal presentations and dinners at the annual meeting, Intelligent Systems in Molecular Biology ([http://www.iscb.org/conf_edu.shtml ISMB]), the official conference of [http://www.iscb.org/ ISCB]<br />
<br><br><br />
Please browse, add and participate in the wiki and the discussion lists. To edit the wiki, create a New Account and then edit the [[BioWiki:Community Portal]] to add a link for your core facility and its description.<br />
<br />
== Wiki page links ==<br />
*[[Call Minutes]]: Detailed minutes from quarterly conference calls on selected and pertinent topics, and annual meetings complete with presenations<br />
*[[BioWiki:Community Portal]]: list your organization!<br />
*[http://www.bioinfo-core.org/index.php/Category:Presentations Presentations]: materials used in presentations related to bioinformatics cores<br />
*[[Ongoing Discussions]]: discussion forums including lists of software, tools, etc.<br />
*[[Special:Categories]]: find pages using categories such as Tools, NextGenSequencing etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=Main_Page&diff=4079Main Page2008-10-11T09:55:56Z<p>Rebhan: /* Wiki page links */</p>
<hr />
<div>'''Welcome to the bioinfo-core's wiki!''' <br />
<br />
== Introduction ==<br />
<br />
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. Through this wiki and our online [http://lists.open-bio.org/mailman/listinfo/bioinfo-core discussion lists] we discuss many topics that are challenging bioinformatics cores world wide. From IT, new instrumentation, staffing and training bioinformaticians, tools, software, to services for biologists and MD's.<br />
<BR><BR><br />
We hold several events throughout the year including quarterly conference calls (with published [[Call Minutes]]) and a yearly set of informal presentations and dinners at the annual meeting, Intelligent Systems in Molecular Biology ([http://www.iscb.org/conf_edu.shtml ISMB]), the official conference of [http://www.iscb.org/ ISCB]<br />
<br><br><br />
Please browse, add and participate in the wiki and the discussion lists. To edit the wiki, create a New Account and then edit the [[BioWiki:Community Portal]] to add a link for your core facility and its description.<br />
<br />
== Wiki page links ==<br />
*[[Call Minutes]]: Detailed minutes from quarterly conference calls on selected and pertinent topics, and annual meetings complete with presenations<br />
*[[BioWiki:Community Portal]]: list your organization!<br />
*[http://www.bioinfo-core.org/index.php/Category:Presentations Presentations]: materials used in presentations related to bioinformatics cores<br />
*[[Ongoing Discussions]]: discussion forums including lists of software, tools, etc.<br />
*[[Special:Categories Browse Categories]]: find pages using categories such as Tools, NextGenSequencing etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_next-gen_sequencing&diff=4077ISMB 2008: BoF on next-gen sequencing2008-10-11T09:54:04Z<p>Rebhan: ISMB 2008: BoF on best practices moved to ISMB 2008: BoF on next-gen sequencing</p>
<hr />
<div>=ISMB2008 BoF: Next-Generation Sequencing: An Introduction and Practical Aspects of Running a Core=<br />
Organizer: David Sexton<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. This one hour BoF attracted much interest from the community and consisted of 4 talks and a panel discussion. Please find slide decks below.<br />
<br />
'''Description:''' This session is geared towards support issues related to next gen sequencing and will include short talks on how to set up the infrastructure, LIMs systems for handling the data, and software tools for working with the data. Ample time will be allotted for discussion.<br />
<br />
'''Presenters:'''<br />
*1) Hemant Kelkar - University of North Carolina - setting up the infrastructure - has 4 to 5 months experience<br />
**[[Media:Kelkar_ismb.pdf]]<br />
*2) Dawei Lin - UC Davis - LIMs based system for cores<br />
**[[Media:ISMB2008_Dawei_Lin.pdf]]<br />
*3) David Sexton - Vanderbilt U - software suite from UCLA ('''postponed for panel discussion session''')<br />
*4) Laxman Iyer - Tufts U - report from next-gen sequencing SIG<br />
<br />
[[Category: presentations]] [[Category:NextGenSequencing]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices&diff=4078ISMB 2008: BoF on best practices2008-10-11T09:54:04Z<p>Rebhan: ISMB 2008: BoF on best practices moved to ISMB 2008: BoF on next-gen sequencing</p>
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<div>#REDIRECT [[ISMB 2008: BoF on next-gen sequencing]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4076ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:53:13Z<p>Rebhan: /* ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility */</p>
<hr />
<div>'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[[Category: presentations]] [[Category:NextGenSequencing]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_next-gen_sequencing_cores&diff=4075ISMB 2008: BoF on next-gen sequencing cores2008-10-11T09:52:37Z<p>Rebhan: ISMB 2008: BoF on next-gen sequencing cores moved to ISMB 2008: BoF on best practices in running bioinformatics cores</p>
<hr />
<div>#REDIRECT [[ISMB 2008: BoF on best practices in running bioinformatics cores]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4074ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:52:37Z<p>Rebhan: ISMB 2008: BoF on next-gen sequencing cores moved to ISMB 2008: BoF on best practices in running bioinformatics cores</p>
<hr />
<div>= ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility =<br />
'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[[Category: presentations]] [[Category:NextGenSequencing]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=Category:Education&diff=4073Category:Education2008-10-11T09:50:39Z<p>Rebhan: New page: Education related to bioinformatics</p>
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<div>Education related to bioinformatics</div>Rebhanhttp://bioinfo-core.org/index.php?title=4_February_2008&diff=40724 February 20082008-10-11T09:50:00Z<p>Rebhan: </p>
<hr />
<div>'''Education for Biologists; Tools utilized by Biologists and Cores.'''<br />
<br />
[[Category:Tools]]<br />
[[Category:Education]]<br />
<br />
=Administrative=<br />
== Attendance ==<br />
<br />
(x = introduced themselves. All others RSVP’d):<br />
Hershel Safer<br />
John Rux, Wistar Institute<br />
Lee Watkins JHU<br />
Charlie Whitaker MIT Cancer Research<br />
x Alastair Kerr Edinborough<br />
x David Sexton, Vanderbilt<br />
x Brent Richter, Partners Healthcare MGH/BWH<br />
x Fran Lewitter, Whitehead Institute<br />
x Michael Rebhan<br />
Mauman Maqbool <br />
Aaron Noll Stowers Institute<br />
x Hemant Kelkar UNC<br />
xDavid Tom UNC<br />
xJianping Zen UNC<br />
Monika Wood Promega<br />
x Steve Jennings U of Arkansas, Little Rock<br />
x George Bell, Whitehead Institute<br />
x Jerry Xu Partners Healthcare<br />
x Lakshmanan Iyer (Lax) Tufts University Medical<br />
x Andrea Hoerster BASF Germany<br />
x Amir Karger, Bauer Center Harvard University<br />
x David Lapointe, Umass Medical<br />
x Dawei Lin UC Davis<br />
<br />
<br />
== bionfo-core meeting logistics at ISMB, Toronto. ==<br />
<br />
<br />
Fran—Currently we have 2 BoF sessions scheduled which occur during lunch. There is 1.25 hours allotted for any BoF session. To make best use of the time, some pre-planning of agenda should be accomplished. <br />
Amongst callers, it was agreed that these times presented the best official ISMB meeting opportunities. Additionally, there would be planned a few dinners for informal gatherings and chat.<br />
Open discussion point: hold a meeting after close of ISMB? There is ½ day left after close. No consensus. <br />
<br />
'''Time of Conference Call:''' Voting is available to select a time of day to hold this conference call in the future:<br />
[http://www.doodle.ch/geaakssbs6b7c53e.]<br />
Please visit and add your vote for your choice. A day has been chosen on the site but please ignore (it’s required). We are only voting on the time.<br />
Once a time is selected, we can vote on a specific date.<br />
<br />
===Possible next concall topics (to be held end of April/ beginning in May):===<br />
<br />
1. Discussion of ePHI within a regulatory and compliance governed research environment. Patient Health Information (PHI) is routinely collected and analyzed together with *omic information (e.g. genotype-phenotype interactions) within informatics groups located within medical schools and academic medical centers. Use of online tools and hosting services are also very accessible and provide utility and collaboration opportunities to the academic researcher. Additionally, institutional review boards and institution’s compliance groups have been frequently seeking guidance from informatics core facilities regarding security and best practice given requests. The discussion could encompass the convergence of these environments and experiences with ensuring privacy of ePHI. Uses of survey monkey to collect patient responses, google docs to share spreadsheets of information have been voiced as possible open-access utilities.<br />
<br />
2. large scale analysis and meta-analysis, trick, tips and tools. Similar to this concall discussion, we would focus on practices, techniques, obtain feedback from the “school of hard-knocks”, discuss tools, etc. regarding genotyping chip arrays, whole genome studies, combining disparate data sets during meta-analysis, etc.<br />
<br />
3. Update on Next-generation sequencing technologies. Following on initial discussion during the first bioinfo-core concall, the participants could synch on the latest techniques and tools, particulary in mapping, that have emerged within the scientific community.<br />
<br />
4. Meetings topic—We were not able to discuss this topic during the call--which seminars and meetings are most effective for bioinformatics core staff and scientists to be introduced to the field and to stay up with new developments.<br />
<br />
No other topics were brought forth, but there was interest in ePHI (acknowledging it’s scope does not pertain within a basic research environment utilizing model organisms) and Analysis discussions.<br />
<br />
<br />
=Education For Biologists (Lead by Michael Rebhan):=<br />
<br />
After introduction of topic by Michael Rebhan:<br />
<br />
AH—worked in 2 companies. Found that there were differences in scientist involvement but mainly due to cultural aspects. In first company the scientists learned the command line, but another company this was not the case. Experience shows that scientists do not try to do anything that doesn't resemble an easy google search. Some even learn to do simple command line usage, especially if it’s a few repetitive commands.<br />
<br />
There are training offerings for in-house tools. VectorNTI and another in-house, custom tool is popular. Some scientists have the motivation to learn, but they tend to learn the tools independently.<br />
<br />
'''AK post meeting comments:'''<br />
Typically most of our PhD students & postdocs are able to learn anything, (including command-line) *if* they can see it addressing an immediate need and their training was applied fairly frequently thereafter. Training was of less use where users had infrequent need of the application. Non technical and broad picture idea seminars why and when to search in protein and not DNA space) do have general appeal and work best in a hands-on environment (20min talk - 20min practical) or in a discussion based format.)<br />
<br />
Similarly, the UNC core trains scientists on specific tools.<br />
<br />
DL—Found that it’s beneficial for biologists to know basic knowledge to analyze data. They are able to do these with relative small help. However, large-scale analysis require core assistance.<br />
<br />
AK—overarching factor in training is the biologist’s familiarity with repetitive analysis and then layering on top the laziest ways to that end. Knowledge of the command line fits this paradigm in some cases and there has been acceptance in learning some unix code. Single click answers are very nice for simplicity, but there are those individuals who take on learning tools and techniques themselves.<br />
<br />
MR— Biologists are becoming more comfortable with computers overall, but that doesn’t necessarily mean that they would carefully read what is displayed, carefully consider parameters on forms etc. This can be challenging in a training situation for tools that need careful usage to provide meaningful results. We also found that short courses are most popular, and that personalized training related to urgent problems is most effective.<br />
<br />
FL—the core at Whitehead at one time provided several formal course offerings: a 1 semester course of lectures, a 2-day intensive course, and a 5 mini course series (lecture and hands on). Topics included sequence analysis, protein analysis, Introduction to UNIX, Perl programming, bioperl, RDBMS’s using MySQL, microarray analysis. However, after a few years, a lot of these offerings were dropped due to attendance and preparation needed. Courses/seminars that are still provided and popular are microarray analysis and introduction to experimentation techniques and statistics for biologist. All materials are freely accessible to the community at [http://jura.wi.mit.edu/bio/education/].<br />
<br />
Format has also changed. While once the courses were formal, now providing “Hot Topics” sessions that are specific and targeted 1-hour sessions with online notes posted internally. They have found the scientists interested in learning more are busy and find it hard to commit to a longer session. A recent topic was ”Unix tips and tricks” (how to manipulate large data outside of excel.) . Had 4-5 different labs represented with 12-15 people in attendance. <br />
<br />
SJ--short and sweet courses are most valuable. LAMP (Linux Apache ModPerl/Python, etc) courses seem to get a lot of participating bioinformatics people. Also provide courses on specific tools and usually have hundreds sign up. R statistics package, for example, had 40 people turn out on a Saturday. Most people who come are grad students who need to get into the domain. Some are biologists who are not afraid of the technical. However, there is an unmet need amongst the biologists who need help with tools, but they haven't been able to draw them in yet.<br />
<br />
UNC group--young people adapt better, amazed by grad student skills. However, there is the MS office culture where biologists demand an easy GUI with which to interact.<br />
<br />
== Discussion--How to create students who are much better in bioinformatics skills? ==<br />
<br />
MIT has research focused informatics courses in the biology department, but these are not applied.<br />
<br />
AH—Germany offers bioinformatics for biologist courses. But even if free, there is not a lot of interest or they are too difficult. Instruction of a more general basis in grad school doesn't make a lot of sense as people are motivated especially when there is direct applicability to their own needs and work.<br />
<br />
MR--we can’t expect too much from mainstream biologists, how about people who are in between—those that are very computer savvy and those that need some nurturing.<br />
<br />
AK--can't teach everything to everyone. Short vocational training works in many cases.<br />
<br />
DS—Vanderbilt is more willing to hire staff than train. The institution perceives this to possess more bang for their buck. They have had good success in creating wikis for document sharing to share knowledge amongst themselves. Experience has shown that a lot of people would rather explore and investigate first on their own without having to ask someone. Given this, it’s easier to look something up on a wiki. <br />
Vanderbilt has a lot of success on using the wiki. If they have a new piece of software, the users usually type up directions and it appears on their wiki.<br />
<br />
DL--Education from regular classes teaches theory. researchers need to know details to run certain programs—need to know the practical.<br />
<br />
AH—They found that errors that occur usually encourages all questions to the core. It’s better to work together first for training. It’s usually easy to get biologists to understand correct way of doing something but hard to teaching them how to do it right. <br />
<br />
= Part II: Tools (David Sexton Introduction)=<br />
<br />
This discussion dovetails Part I as we want to discuss tools that enable biologists to perform analysis. Some tools investigated:<br />
<br />
Interproscan [http://www.ebi.ac.uk/InterProScan/]<br />
Galaxy [http://main.g2.bx.psu.edu/]<br />
DS--played with this a little to glue workflows together. Seemed to do well in going to NCBI, do a blast, bring blast results back to workbench to do follow-on analysis. But it appears to be more of a tool for bioinformaticians than biologists. It still requires knowledge of each step than working de-novo.<br />
MR--good experience. groups have used it for large scale analysis. Some are even starting to put their own tools into it, adding them for a limited user audience, its good for large-scale analysis, especially comparisons between datasets (e.g. overlaps between datasets that refer to defined genomic regions with start and stop, such as ChIP-on-chip data with genome annotations)<br />
<br />
Biomart [http://www.biomart.org/]<br />
Geneious [http://www.geneious.com/]<br />
BOSC [http://www.open-bio.org/wiki/Main_Page]<br />
Emboss [http://emboss.sourceforge.net/] <br />
Lax-- GCG is going away, lax has moved to emboss but the migration was hard as the biologists were used to the GCC GUI.<br />
<br />
Taverna [http://taverna.sourceforge.net/] : reliability is not that high. Recommended to bring web service in house. Requires lots of file passing, and if those files are large, this makes it very cumbersome. There could be some solutions to get around this. Lax was surprised when it worked without much effort<br />
AK: Most problems occur with web services not running: having a local copy of said web services is the easiest solution. I use a local copy of Soaplab as it is trivial to add EMBOSS applications (or any command line program with an ACD file) to Soaplab. Seahawk/BioMoby should make this easy as well but I have not tried.<br />
'''N.B.''' main snag is that all files are moved across the network, which makes working with large file sizes almost a no go. This may be fixed in taverna2. Also I have had problems with the taverna client on 64-bit linux systems but I have not tried hard enough to debug this.<br />
<br />
<br />
===Micro-Array tools:===<br />
<br />
Good site for general microarray links:<br />
[http://bioinfo.bgu.ac.il/bsu/microarrays/links/] <br />
<br />
BASE [http://base.thep.lu.se/] <br />
DL--trying to create a database using (second version) from sweden. people can retrieve data from web and have a plugin to. Some folks on the list have tried it.<br />
TM4: [http://www.tm4.org/]: Lax: multiple experiment viewer from TIGR--good for experimentalist.<br />
madmax has gone commercial--no longer open source.<br />
<br />
Webarray? [http://bioinformatics.skcc.org/webarray/] a web based microarray tool wraps around bioconductor and mysql backend.<br />
<br />
Carmaweb [https://carmaweb.genome.tugraz.at/carma/]<br />
<br />
UCdavis uses R package mostly for analysis<br />
<br />
===SNP array analysis===<br />
<br />
chipmonk. [http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/] “A tool to visualize and analyze chip on chip array data. However, they only have certain genomes available in their database. Some have had good experience talk to author who has bee very good at incorporating additional genomes. However the Arabidopsis genome seems to be troublesome.<br />
AK--Simple but useful. Its simplicity has enabled a few users to get to grips with analysing their data without being too confused over multiple options. Author has been good in incorporating genome of interest (yeast).<br />
<br />
Plink [http://pngu.mgh.harvard.edu/~purcell/plink/]. A whole genome association analysis toolset. Analyzes large scale chip arrays. Vanderbilt, Harvard Med uses it. Developed at MGH.<br />
<br />
WASP [http://chgr.mc.vanderbilt.edu/wasp/] from vanderbilt is publicly available.<br />
<br />
Dchip [http://biosun1.harvard.edu/complab/dchip/] --some good usage, some not. Can do some simple analysis.<br />
<br />
===Visualizing structures?===<br />
<br />
pymol--http://pymol.sourceforge.net/<br />
<br />
AK--One of the tools of choice for our structural groups. Loads of powerful feature and well as the capability to generate publication quality figures.<br />
<br />
MAGE and Kinemage: [http://kinemage.biochem.duke.edu/website/kinhome.htm] from Duke. A web based tool to connect structure and display.<br />
<br />
autodoc [http://autodock.scripps.edu/], is very good for docking calculations.</div>Rebhanhttp://bioinfo-core.org/index.php?title=List_of_Software&diff=4071List of Software2008-10-11T09:48:15Z<p>Rebhan: </p>
<hr />
<div>Please enter information about your core facility on the [[BioWiki:Community Portal]]. <br />
<br />
[[Category:Tools]]<br />
<br />
<br><br />
<hr><br />
<h2>Tools popular with biologists</h2><br />
<br>This is a list of the tools that were mentioned in our discussion on "bioinformatics for the biologists" on Feb 4th, 2008.<br />
<br><br><br />
<h3>Microarray data retrieval and basic analysis</h3><br />
<ul><br />
<li>[http://base.thep.lu.se BASE] from Lund University, Sweden (basic analysis and database)<br />
<li>[http://www.tm4.org/ Multiple Experiment Viewer from Quackenbush Group at Harvard Univ]<br />
<li>[http://bioinformatics.skcc.org/webarray/ WebArray: Web interface, based on bioconductor and mySQL]<br />
<li>[https://carmaweb.genome.tugraz.at/carma CarmaWeb]<br />
<li>[http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ ChipMonk] for ChIP-on-chip data, e.g. from Nimblegen<br />
<li>[http://biosun1.harvard.edu/complab/dchip/ DChip]: basic analysis (e.g. get a list of differentially expressed genes)<br />
<li>[http://bioinfo.bgu.ac.il/bsu/microarrays/links/ A good links site] for multiple applications<br />
</ul><br />
<h3>Structure visualization and basic analysis</h3><br />
<ul><br />
<li>[http://pymol.sourceforge.net/ PyMOL]<br />
<li>AutoDock for docking<br />
<li>DiscoveryStudio (?)<br />
<li>[http://kinemage.biochem.duke.edu Kinmage] for 3D Macromolecule analysis from Richardson Lab at Duke<br />
<li>[http://swissmodel.expasy.org/spdbv/ DeepView] for structure analysis and modeling from the Swiss Institute of Bioinformatics and GlaxoSmithKline R&D<br />
<li>[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D] for structure veiwer from NCBI<br />
</ul><br />
<h3>Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data</h3><br />
<ul><br />
<li>[http://cytoscape.org/ Cytoscape]<br />
<li>[http://reactome.org/ Reactome] including [http://www.reactome.org/cgi-bin/skypainter2?DB=gk_current Skypainter] and the latest biomart interface [http://brie8.cshl.org/cgi-bin/mart Reactome Mart]<br />
<li>[http://www.bioinformatics.ed.ac.uk/epe/ EPE] Edinburgh Pathway Editor<br />
</ul><br />
<h3>Pipeline Tools</h3><br />
<ul><br />
<li>[http://taverna.sourceforge.net/ Taverna] Best uses in conjunction with in-house web services to ensure reliability. Most command line applications can be converted to a web service using [http://wwww.ebi.ac.uk/soaplab/ Soaplab]. Version 2 of taverna should handle large file sizes a lot better.<br />
<li>[http://galaxy.psu.edu/ Galaxy] This package is from Penn State and is very good.<br />
<li> [http://www.biomedcentral.com/1471-2105/8/208 Alternatives:] A paper highlighting Seahawk ([http://biomoby.org/ Biomoby]) but also mentions both Taverna and Remora <br />
</ul><br />
<br />
<hr><br />
<h3>Looking for collaborations in Rosetta Resolver training</h3><br />
The National Institute of Biotechnology is experimenting with Rosetta in setting up a national test-bed for bioinformatics software. As a part of this collaboration, we are trying to develop a training strategy that would allow researchers, both industry and academia, figure out the value of Resolver for their research with minimal training.<p><br />
We are looking for someone interested in developing together training material for people who understand microarray analysis, at least the basics of it, and wish to get rapidly started with Resolver.<p><br />
Eitan Rubin, [mailto:erubin@bgu.ac.il erubin@bgu.ac.il]<br />
<hr><br />
<br />
<hr><br />
<center>Return to [http://www.bioinfo-core.org Bioinfo-core wiki]</center><br />
<br />
<hr></div>Rebhanhttp://bioinfo-core.org/index.php?title=Category:Tools&diff=4070Category:Tools2008-10-11T09:47:37Z<p>Rebhan: New page: Tools related to bioinformatics, including software, web servers, web services and other resources.</p>
<hr />
<div>Tools related to bioinformatics, including software, web servers, web services and other resources.</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_next-gen_sequencing&diff=4068ISMB 2008: BoF on next-gen sequencing2008-10-11T09:46:01Z<p>Rebhan: </p>
<hr />
<div>=ISMB2008 BoF: Next-Generation Sequencing: An Introduction and Practical Aspects of Running a Core=<br />
Organizer: David Sexton<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. This one hour BoF attracted much interest from the community and consisted of 4 talks and a panel discussion. Please find slide decks below.<br />
<br />
'''Description:''' This session is geared towards support issues related to next gen sequencing and will include short talks on how to set up the infrastructure, LIMs systems for handling the data, and software tools for working with the data. Ample time will be allotted for discussion.<br />
<br />
'''Presenters:'''<br />
*1) Hemant Kelkar - University of North Carolina - setting up the infrastructure - has 4 to 5 months experience<br />
**[[Media:Kelkar_ismb.pdf]]<br />
*2) Dawei Lin - UC Davis - LIMs based system for cores<br />
**[[Media:ISMB2008_Dawei_Lin.pdf]]<br />
*3) David Sexton - Vanderbilt U - software suite from UCLA ('''postponed for panel discussion session''')<br />
*4) Laxman Iyer - Tufts U - report from next-gen sequencing SIG<br />
<br />
[[Category: presentations]] [[Category:NextGenSequencing]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=Category:NextGenSequencing&diff=4066Category:NextGenSequencing2008-10-11T09:43:55Z<p>Rebhan: New page: Pages related to next-generation sequencing</p>
<hr />
<div>Pages related to next-generation sequencing</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4065ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:43:33Z<p>Rebhan: /* Presenters: */</p>
<hr />
<div>= ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility =<br />
'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[[Category: presentations]] [[Category:NextGenSequencing]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=BioWiki:Community_Portal&diff=4063BioWiki:Community Portal2008-10-11T09:39:17Z<p>Rebhan: </p>
<hr />
<div>[[Ongoing Discussions]] | [[Call Minutes]] | [[Core page template]]<br />
<br />
<h2>Bioinfo-Core Member Institutions</h2><br />
To add your facility, please link to a description you have on the internet or add a page to this wiki. Please follow the [[Core page template]].<br />
<br />
'''List of Bioinformatics Core Facilities'''<br />
<br />
*[http://jura.wi.mit.edu/bio/general.html Bioinformatics and Research Computing (BaRC)], Whitehead Institute (USA)<br />
*[http://bsu.ncl.ac.uk/general.html Newcastle University Bioinformatics Support Unit] (UK)<br />
*[http://cbsu.tc.cornell.edu/cbsu_bioinfo_core.html Computational Biology Service Unit], Cornell University (USA)<br />
*[http://chgr.mc.vanderbilt.edu/page/computational-genomics-core Computational Genomics Core], Center for Human Genetics Research, Vanderbilt University (USA)<br />
*[http://bioinformatics.unc.edu Center for Bioinformatics], University of North Carolina at Chapel Hill (USA)<br />
*[http://www.tufts.edu/sackler/neuroscience/CNR/bioinformatics.html Genomics Core], Center for Neuroscience Research, Tufts Univ School of Medicine (USA)<br />
*[[Bioinformatics Group]], Promega Corp. (USA)<br />
*[http://bioinformatics.ucdavis.edu Bioinformatics Core], UC Davis Genome Center (USA)<br />
*[http://bifx1.bio.ed.ac.uk/wiki/index.php/Bioinformatics_Core_Facilities Bioinformatics Core Facility], Wellcome Trust Centre for Cell Biology, University of Edinburgh (UK)<br />
*[http://www.radium.no/core/index.php?section=3 Bioinformatics Core], Rikshospitalet-Radiumhospitalet and University of Oslo (Norway)<br />
*[http://bioinformatics.ualr.edu/mbc MidSouth Bioinformatics Center], University of Arkansas at Little Rock (USA)<br />
*[http://bioinformatics.salk.edu/core.html Salk Institute Bioinformatics], San Diego, CA (USA)<br />
*[http://www.fmi.ch/html/technical_resources/bioinformatics/bioinformatics.html Friedrich Miescher Institute for Biomedical Research], Novartis Research Foundation, Basel (Switzerland)<br />
*[http://bioinfo.bgu.ac.il Bioinformatics Core Facility], National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev (Israel)<br />
*[http://bioinformatics.unl.edu/ Bioinformatics Core Research Facility], Center for Biotechnology, University of Nebraska-Lincoln, Lincoln (USA)<br />
*[http://www.giga.ulg.ac.be/extranet/services.htm Bioinformatics Facility], GIGA (Interdisciplinary Cluster for Applied Genoproteomics), University of Liege (BE)<br />
*[[Babraham Bioinformatics, The Babraham Institute, Cambridge]] (UK)<br />
*[http://web.mit.edu/ccr/core/facilities/bioinformatics/ Bioinformatics and Computing Core Facility (BCC)], Koch Institute - MIT Cambridge, MA (USA)<br />
*[[ERIS]] Partners Healthcare/Harvard Medical School Enterprise Research Infrastructure and Systems, Boston MA</div>Rebhanhttp://bioinfo-core.org/index.php?title=Next-Gen_Sequencing&diff=4062Next-Gen Sequencing2008-10-11T09:37:45Z<p>Rebhan: /* Next Generation Sequencing */</p>
<hr />
<div>== Next Generation Sequencing ==<br />
<br />
* ISMB 2008: See the [http://www.bioinfo-core.org/index.php/ISMB_2008:_notes ISMB 2008 notes] and the presentations given at the [http://www.bioinfo-core.org/index.php/20_July_2008 BoF on next-gen sequencing] (An Introduction and Practical Aspects of Running a Core)<br />
* [[Call Minutes]]: some are related to next-gen sequencing</div>Rebhanhttp://bioinfo-core.org/index.php?title=Next-Gen_Sequencing&diff=4061Next-Gen Sequencing2008-10-11T09:37:20Z<p>Rebhan: </p>
<hr />
<div>== Next Generation Sequencing ==<br />
<br />
* ISMB 2008: See the [http://www.bioinfo-core.org/index.php/ISMB_2008:_notes ISMB 2008 notes] and the presentations given at the [http://www.bioinfo-core.org/index.php/20_July_2008 BoF on next-gen sequencing] (An Introduction and Practical Aspects of Running a Core)<br />
* [[Call_Minutes Call minutes]]: some are related to next-gen sequencing</div>Rebhanhttp://bioinfo-core.org/index.php?title=Main_Page&diff=4060Main Page2008-10-11T09:33:33Z<p>Rebhan: /* Wiki page links */</p>
<hr />
<div>'''Welcome to the bioinfo-core's wiki!''' <br />
<br />
== Introduction ==<br />
<br />
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. Through this wiki and our online [http://lists.open-bio.org/mailman/listinfo/bioinfo-core discussion lists] we discuss many topics that are challenging bioinformatics cores world wide. From IT, new instrumentation, staffing and training bioinformaticians, tools, software, to services for biologists and MD's.<br />
<BR><BR><br />
We hold several events throughout the year including quarterly conference calls (with published [[Call Minutes]]) and a yearly set of informal presentations and dinners at the annual meeting, Intelligent Systems in Molecular Biology ([http://www.iscb.org/conf_edu.shtml ISMB]), the official conference of [http://www.iscb.org/ ISCB]<br />
<br><br><br />
Please browse, add and participate in the wiki and the discussion lists. To edit the wiki, create a New Account and then edit the [[BioWiki:Community Portal]] to add a link for your core facility and its description.<br />
<br />
== Wiki page links ==<br />
*[[Call Minutes]]: Detailed minutes from quarterly conference calls on selected and pertinent topics, and annual meetings complete with presenations<br />
*[[BioWiki:Community Portal]]: list your organization!<br />
*[http://www.bioinfo-core.org/index.php/Category:Presentations Presentations]: materials used in presentations related to bioinformatics cores<br />
*[[Ongoing Discussions]]: discussion forums including lists of software, tools, etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=Main_Page&diff=4059Main Page2008-10-11T09:33:08Z<p>Rebhan: /* Wiki page links */</p>
<hr />
<div>'''Welcome to the bioinfo-core's wiki!''' <br />
<br />
== Introduction ==<br />
<br />
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. Through this wiki and our online [http://lists.open-bio.org/mailman/listinfo/bioinfo-core discussion lists] we discuss many topics that are challenging bioinformatics cores world wide. From IT, new instrumentation, staffing and training bioinformaticians, tools, software, to services for biologists and MD's.<br />
<BR><BR><br />
We hold several events throughout the year including quarterly conference calls (with published [[Call Minutes]]) and a yearly set of informal presentations and dinners at the annual meeting, Intelligent Systems in Molecular Biology ([http://www.iscb.org/conf_edu.shtml ISMB]), the official conference of [http://www.iscb.org/ ISCB]<br />
<br><br><br />
Please browse, add and participate in the wiki and the discussion lists. To edit the wiki, create a New Account and then edit the [[BioWiki:Community Portal]] to add a link for your core facility and its description.<br />
<br />
== Wiki page links ==<br />
*[[Call Minutes]]: Detailed minutes from quarterly conference calls on selected and pertinent topics, and annual meetings complete with presenations<br />
*[[BioWiki:Community Portal]]: list your organization!<br />
*[[http://www.bioinfo-core.org/index.php/Category:Presentations]]: materials used in presentations related to bioinformatics cores<br />
*[[Ongoing Discussions]]: discussion forums including lists of software, tools, etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=Main_Page&diff=4058Main Page2008-10-11T09:30:55Z<p>Rebhan: /* Wiki page links */</p>
<hr />
<div>'''Welcome to the bioinfo-core's wiki!''' <br />
<br />
== Introduction ==<br />
<br />
Bioinfo-core is a worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas. Through this wiki and our online [http://lists.open-bio.org/mailman/listinfo/bioinfo-core discussion lists] we discuss many topics that are challenging bioinformatics cores world wide. From IT, new instrumentation, staffing and training bioinformaticians, tools, software, to services for biologists and MD's.<br />
<BR><BR><br />
We hold several events throughout the year including quarterly conference calls (with published [[Call Minutes]]) and a yearly set of informal presentations and dinners at the annual meeting, Intelligent Systems in Molecular Biology ([http://www.iscb.org/conf_edu.shtml ISMB]), the official conference of [http://www.iscb.org/ ISCB]<br />
<br><br><br />
Please browse, add and participate in the wiki and the discussion lists. To edit the wiki, create a New Account and then edit the [[BioWiki:Community Portal]] to add a link for your core facility and its description.<br />
<br />
== Wiki page links ==<br />
*[[Call Minutes]]: Detailed minutes from quarterly conference calls on selected and pertinent topics, and annual meetings complete with presenations<br />
*[[BioWiki:Community Portal]]: list your organization!<br />
*[[Category:Presentations]]: materials used in presentations related to bioinformatics cores<br />
*[[Ongoing Discussions]]: discussion forums including lists of software, tools, etc.</div>Rebhanhttp://bioinfo-core.org/index.php?title=Category:Presentations&diff=4057Category:Presentations2008-10-11T09:29:41Z<p>Rebhan: New page: Here we share materials used in presentations related to bioinformatics cores.</p>
<hr />
<div>Here we share materials used in presentations related to bioinformatics cores.</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4055ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:28:36Z<p>Rebhan: 22 July 2008 moved to ISMB 2008: BoF on next-gen sequencing cores</p>
<hr />
<div>= ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility =<br />
'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[[Category: presentations]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=22_July_2008&diff=405622 July 20082008-10-11T09:28:36Z<p>Rebhan: 22 July 2008 moved to ISMB 2008: BoF on next-gen sequencing cores</p>
<hr />
<div>#REDIRECT [[ISMB 2008: BoF on next-gen sequencing cores]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_next-gen_sequencing&diff=4053ISMB 2008: BoF on next-gen sequencing2008-10-11T09:27:55Z<p>Rebhan: 20 July 2008 moved to ISMB 2008: BoF on best practices</p>
<hr />
<div>=ISMB2008 BoF: Next-Generation Sequencing: An Introduction and Practical Aspects of Running a Core=<br />
Organizer: David Sexton<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. This one hour BoF attracted much interest from the community and consisted of 4 talks and a panel discussion. Please find slide decks below.<br />
<br />
'''Description:''' This session is geared towards support issues related to next gen sequencing and will include short talks on how to set up the infrastructure, LIMs systems for handling the data, and software tools for working with the data. Ample time will be allotted for discussion.<br />
<br />
'''Presenters:'''<br />
*1) Hemant Kelkar - University of North Carolina - setting up the infrastructure - has 4 to 5 months experience<br />
**[[Media:Kelkar_ismb.pdf]]<br />
*2) Dawei Lin - UC Davis - LIMs based system for cores<br />
**[[Media:ISMB2008_Dawei_Lin.pdf]]<br />
*3) David Sexton - Vanderbilt U - software suite from UCLA ('''postponed for panel discussion session''')<br />
*4) Laxman Iyer - Tufts U - report from next-gen sequencing SIG<br />
<br />
[[Category: presentations]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=20_July_2008&diff=405420 July 20082008-10-11T09:27:55Z<p>Rebhan: 20 July 2008 moved to ISMB 2008: BoF on best practices</p>
<hr />
<div>#REDIRECT [[ISMB 2008: BoF on best practices]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_next-gen_sequencing&diff=4052ISMB 2008: BoF on next-gen sequencing2008-10-11T09:26:20Z<p>Rebhan: /* ISMB2008 BoF: Next-Generation Sequencing: An Introduction and Practical Aspects of Running a Core */</p>
<hr />
<div>=ISMB2008 BoF: Next-Generation Sequencing: An Introduction and Practical Aspects of Running a Core=<br />
Organizer: David Sexton<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. This one hour BoF attracted much interest from the community and consisted of 4 talks and a panel discussion. Please find slide decks below.<br />
<br />
'''Description:''' This session is geared towards support issues related to next gen sequencing and will include short talks on how to set up the infrastructure, LIMs systems for handling the data, and software tools for working with the data. Ample time will be allotted for discussion.<br />
<br />
'''Presenters:'''<br />
*1) Hemant Kelkar - University of North Carolina - setting up the infrastructure - has 4 to 5 months experience<br />
**[[Media:Kelkar_ismb.pdf]]<br />
*2) Dawei Lin - UC Davis - LIMs based system for cores<br />
**[[Media:ISMB2008_Dawei_Lin.pdf]]<br />
*3) David Sexton - Vanderbilt U - software suite from UCLA ('''postponed for panel discussion session''')<br />
*4) Laxman Iyer - Tufts U - report from next-gen sequencing SIG<br />
<br />
[[Category: presentations]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_next-gen_sequencing&diff=4051ISMB 2008: BoF on next-gen sequencing2008-10-11T09:25:02Z<p>Rebhan: /* ISMB2008 BoF: Next-Generation Sequencing: An Introduction and Practical Aspects of Running a Core */</p>
<hr />
<div>=ISMB2008 BoF: Next-Generation Sequencing: An Introduction and Practical Aspects of Running a Core=<br />
Organizer: David Sexton<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. This one hour BoF attracted much interest from the community and consisted of 4 talks and a panel discussion. Please find slide decks below.<br />
<br />
'''Description:''' This session is geared towards support issues related to next gen sequencing and will include short talks on how to set up the infrastructure, LIMs systems for handling the data, and software tools for working with the data. Ample time will be allotted for discussion.<br />
<br />
'''Presenters:'''<br />
*1) Hemant Kelkar - University of North Carolina - setting up the infrastructure - has 4 to 5 months experience<br />
**[[Media:Kelkar_ismb.pdf]]<br />
*2) Dawei Lin - UC Davis - LIMs based system for cores<br />
**[[Media:ISMB2008_Dawei_Lin.pdf]]<br />
*3) David Sexton - Vanderbilt U - software suite from UCLA ('''postponed for panel discussion session''')<br />
*4) Laxman Iyer - Tufts U - report from next-gen sequencing SIG<br />
<br />
[[Category: presentations]]<br />
[[Category: meeting]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4050ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:24:17Z<p>Rebhan: /* Presenters: */</p>
<hr />
<div>= ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility =<br />
'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[[Category: presentations]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4049ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:23:51Z<p>Rebhan: /* Presenters: */</p>
<hr />
<div>= ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility =<br />
'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[[Category: presentations, meetings]]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4048ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:22:37Z<p>Rebhan: /* Presenters: */</p>
<hr />
<div>= ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility =<br />
'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[Category: presentations]</div>Rebhanhttp://bioinfo-core.org/index.php?title=ISMB_2008:_BoF_on_best_practices_in_running_bioinformatics_cores&diff=4047ISMB 2008: BoF on best practices in running bioinformatics cores2008-10-11T09:21:54Z<p>Rebhan: </p>
<hr />
<div>= ISMB2008 BoF: Best Practices for Running a Bioinformatics Core Facility =<br />
'''Organizer:''' Fran Lewitter<br />
<br />
<br />
This in-person session has held during the annual ISMB meeting in Toronto Canada. There was great interest in this topic with many individuals, departements and universities beginning core services. Please find presentations below.<br />
<br />
====Description: ====<br />
We have met annually since 2002 and have participated in conference calls since ISMB/ECCB 2007. Today's meeting will address best practices for running a bioinformatics core facility and will include short talks from people from different types of facilities - universities (public and private), research institutes, and industry. Ample time will be allotted for discussion.<br />
<br />
====Presenters: ====<br />
*1) David Sexton - Vanderbilt U - mid-sized private university<br />
**[[Media:Sexton_ISMB08.pdf]]<br />
*2) Dawei Lin - UC Davis - large state university<br />
**[[Media:Lin_ISMB2008.pdf]]<br />
*3) Simon Andrews - The Babraham Institute - small research Institute in the UK<br />
**[[Media:Andrews_ismb2008.pdf]]<br />
*4) Steve Jennings - University of Arkansas at Little Rock - academic NIH funded Bioinformatics core<br />
**[[Media:Jennings_ISMB2008.pdf]]<br />
*5) Michael Rebhan - Novartis - industry<br />
**[[Media:rebhan_ismb08.pdf]]<br />
<br />
<br />
Search term in web browser: bioinfo-core<br />
Email - [http://open-bio.org/mailman/listinfo/bioinfo-core]<br />
Wiki - [http://www.bioinfo-core.org/]<br />
<br />
Discussion:<br />
Panelists consisted of all Presenters.<br />
Questions to get started:<br />
*How do you and your staff keep up with new scientific knowledge?<br />
*What are your greatest challenges in the next year?<br />
*What wisdom can you offer with respect hiring staff?<br />
<br />
[Category: presentations, meetings]</div>Rebhanhttp://bioinfo-core.org/index.php?title=Next-Gen_Sequencing&diff=4046Next-Gen Sequencing2008-10-11T09:19:32Z<p>Rebhan: </p>
<hr />
<div>== Next Generation Sequencing ==<br />
<br />
* See the [http://www.bioinfo-core.org/index.php/ISMB_2008:_notes ISMB 2008 notes] and the presentations given at the [http://www.bioinfo-core.org/index.php/20_July_2008 BoF on next-gen sequencing] (An Introduction and Practical Aspects of Running a Core)</div>Rebhanhttp://bioinfo-core.org/index.php?title=Next-Gen_Sequencing&diff=4045Next-Gen Sequencing2008-10-11T09:18:58Z<p>Rebhan: </p>
<hr />
<div>== Next Generation Sequencing ==<br />
<br />
* See the [http://www.bioinfo-core.org/index.php/ISMB_2008:_notes ISMB 2008 notes] and the presentations given at the [http://www.bioinfo-core.org/index.php/20_July_2008 BoF on next-gen sequencing]</div>Rebhanhttp://bioinfo-core.org/index.php?title=Next-Gen_Sequencing&diff=4044Next-Gen Sequencing2008-10-11T09:15:59Z<p>Rebhan: </p>
<hr />
<div>== Next Generation Sequencing ==<br />
<br />
* See the [http://www.bioinfo-core.org/index.php/ISMB_2008:_notes ISMB 2008 notes]</div>Rebhan