tag:blogger.com,1999:blog-65418925553277356372024-03-15T10:03:19.541-07:00FishBlog | Zebrafish Genomics and Community AnnotationAnnouncement Blog for the Zebrafish Genome Annotation Project at the Institute of Genomics and Integrative Biology (IGIB - CSIR).
The Blog posts are personal opinion and does not reflect that of their employers or associated organisations.<a href="http://orthoquiz.blogspot.com/">IndiMedicos OrthoQuiz</a>Unknownnoreply@blogger.comBlogger18125tag:blogger.com,1999:blog-6541892555327735637.post-14493508819187328862009-01-21T11:03:00.000-08:002009-01-21T11:07:03.388-08:00Zebrafish GenomeWiki has gone LIVEZebrafish GenomeWiki has gone live today.<br /><br />A flyer describing the features of the Zebrafish GenomeWiki and a request for community participation can be downloaded from the home page of the Zebrafish GenomeWiki.SSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com20tag:blogger.com,1999:blog-6541892555327735637.post-74584248903864478632009-01-18T05:41:00.000-08:002009-01-18T05:54:07.179-08:00Zebrafish GenomeWiki gets a new address<span style="font-size:130%;">The Zebrafish GenomeWiki Beta Preview version is now available at<br /><br /><a href="http://fishwiki.igib.res.in">http://fishwiki.igib.res.in</a><br /><br />It can also be viewed at its older address<br /><br /><a href="http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WebHome">http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WebHome</a></span>SSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-85957706359305436462009-01-17T10:09:00.000-08:002009-01-17T10:50:28.711-08:00Zebrafish GenomeWiki unleashes its WikiPower<span style="font-weight: bold;font-size:130%;" >Manually curated gene list</span><br /><br />Over the last few days we have manually curated/edited over 200 genes. Manual curation includes information regarding Gene description, Gene Function, Gene Cloning, Gene Structure, Disorders and Mutations, and Related <span class="twikiNewLink">PubMed </span>articles.<br /><br />These genes are listed separately and can be viewed through the ALL MANUALLY CURATED GENES link on the right hand side banner of the Zebrafish GenomeWiki home page. The link is also available at<br /><br /><a href="http://fishwiki.igib.in/TWiki_4_2_4/bin/view/ZebrafishGenome/WebHome">http://fishwiki.igib.in/TWiki_4_2_4/bin/view/ZebrafishGenome/WebHome</a><br /><br />Watch this space for more manually curated gene in the near future.<br /><span style="font-weight: bold;font-size:130%;" >Hail to the WikiPower!!</span>SSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-65615484366803549082009-01-17T05:20:00.000-08:002009-01-17T05:38:38.674-08:00Learn Your Way Around Zebrafish GenomeWikiA Short guide entitled Learn Your Way Around Zebrafish GenomeWiki is available for new users. The guide can be viewed at<br /><br /><a href="http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WayAroundFishWiki">http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WayAroundFishWiki</a><br /><br />The guide provides basic information on why this project was initiated and also provides a brief description of the ultimate goal of the project. In addition it also provides brief information on the following topics such as:<br /><br />- Browsing and registering at the Zebrafish GenomeWiki<br />- Finding your favorite gene on the Zebrafish GenomeWiki<br />- Annotating / Editing the contents of the Zebrafish GenomeWiki<br />- Who can contribute/ annotate on the Zebrafish GenomeWiki?<br />- How to annotate/edit your favorite gene?<br />- A short tutorial on TWiki.SSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-79036754373856759962009-01-17T00:17:00.000-08:002009-01-17T00:36:29.185-08:00<span style="font-weight: bold;">Zebrafish GenomeWiki Beta Preview</span><br /><br />Zebrafish GenomeWiki is a shared genomics resource for community annotation of the Zebrafish genome on the lines of the “Wikipedia”. Members of the Zebrafish community can create new data sets, annotate, comment and edit existing data sets using the Zebrafish GenomeWiki portal. The Zebrafish GenomeWiki will permit community experts and individual investigators to add the latest genomics information and discuss alternative annotations in real time there by speeding up the fine annotation the Zebrafish genome. Currently there are over 3 x 10^5 documents in the Zebrafish GenomeWiki and we are still growing!!<br /><br />The Zebrafish GenomeWiki Beta Preview version is now available at<br /><br /><a href="http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WebHome">http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WebHome</a><br /><br />Please Note: We are still working on the portal and many obvious thinks need to be fixed including the Search tool.SSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-14042931138578581622009-01-14T21:53:00.000-08:002009-01-14T21:57:44.170-08:00Zebrafish GenomeWiki Beta Preview<a href="http://fishwiki.igib.res.in/TWiki_4_2_4/bin/view/Main/WebHome"> <img style="width: 584px; height: 70px;" src="http://sites.google.com/a/rnabiology.org/vinodscaria/lab-members--collaborators/zebrafish_genomeWiki.gif" border="0" /></a><br /><br /><a href="http://fishwiki.igib.res.in/TWiki_4_2_4/bin/view/Main/WebHome">Zebrafish GenomeWiki Beta Preview version is now available to the community. </a><br /><br />We are still working on the portal and many obvious thinks need to be fixed including the Search tool. We have been trying to crawl the site using swish-e but it seems the site has grown so huge (3*10^5 documents and growing).Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-25094081921795443772008-09-24T04:29:00.000-07:002008-09-24T04:36:24.042-07:00Zebrafish GenomeWiki Beta PreviewThe Zebrafish <a href="http://fishwiki.igib.in">GenomeWiki Beta preview is available at http://fishwiki.igib.in<br /></a>we are still working on the system and there are many more bugs to find than we can fix :)<br /><br />The system is a bit too slow at the moment, but sure, it will hopefully get faster when we will move to our new production server.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-85153383074959670782008-08-03T22:25:00.000-07:002008-08-03T22:32:46.754-07:00Trip to Sultanpur<p>Here is a link to view pictures of FishMap Team's Day Out.</p><p>Well FishMap team do post ur comments:)..</p><p><a href="http://picasaweb.google.com/meenakshish/FishMapTeamOnAHolidayToSultanpur">http://picasaweb.google.com/meenakshish/FishMapTeamOnAHolidayToSultanpur</a></p>Meenakshi Sharmahttp://www.blogger.com/profile/00587951094644637499noreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-4872564836084780962008-06-14T05:23:00.000-07:002008-06-14T05:40:54.927-07:00Zebrafish Genome Wiki > Vision<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZu8PyOR6uFffr-rbh34E1WatJtxRZKEGpU4kJLrmuvln_gwjhR0KSRebSqdvOgeLiIAQ86XNLu3Icbby4MRNzOHVL7Tc8AuvAAKqAkl3EfnV5W85KE9UlMUfRbVvlY7OJ2F4Oe9hjfadO/s1600-h/vision.gif"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZu8PyOR6uFffr-rbh34E1WatJtxRZKEGpU4kJLrmuvln_gwjhR0KSRebSqdvOgeLiIAQ86XNLu3Icbby4MRNzOHVL7Tc8AuvAAKqAkl3EfnV5W85KE9UlMUfRbVvlY7OJ2F4Oe9hjfadO/s400/vision.gif" alt="" id="BLOGGER_PHOTO_ID_5211712954280507106" border="0" /></a><br />I had blogged about the <a href="http://miracle.igib.res.in/fishwiki">Zebrafish GenomeWiki a</a><span style="text-decoration: underline;"> </span>couple of days back and people had been asking what is the vision or blueprint for the system.<br /><br />I had put up a schematic representation on what would the system be for the Zebrafish Genome Community. I am replicating it with this post.<br /><br /><br /><br />So I thought I would compile them for you.<br /><br />What we WOULD be doing<br /><br />Create a portal for community annotation of the Zebrafish Genome.o<br />Create a Wiki based solution and see how it works for community annotation of genomics data (nobody has created one so far !)<br />Create a vibrant community that would help understand the Biology of this unique model organism better<br />Create a system for giving credits to participants in Community Annotation<br />Make available the entire data for bulk download and data mining<br />Work towards standards for data definitions and free and collaborative annotation<br />Work towards open standards for content syndication across databases and tools.<br /><br />What we WOULD NOT BE trying to do<br /><br />Compete with existing databases (We think what is already there is really good !)<br /><br /><br />We are currently working on a system to assign credits to individuals or groups of individuals (for eg: a Lab) for community annotation of data. We have different models in place and I do not know of many people working on the topic other than the <a href="http://blogs.nature.com/ng/freeassociation/2008/03/microattribution_for_community_1.html">Nature team.</a><br /><br />We would highly appreciate your ideas and views on the topic. Post them as a comment or e-mail me at vinods[at]igib.inUnknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-85657005601159729152008-06-12T01:01:00.001-07:002008-06-12T01:17:16.056-07:00The Zebrafish GenomeWikiAfter creating FishMap, we are rather busy giving the final finishing touches to one of the major systems in our blueprint for Zebrafish Genomics.<br /><br />We had earlier petnamed it FishWiki, and now we have decided to call it <img src="file:///C:/DOCUME%7E1/vinods/LOCALS%7E1/Temp/moz-screenshot-4.jpg" alt="" /><a href="http://miracle.igib.res.in/fishwiki"> Zebrafish GenomeWiki.</a><br /><br />Much has been written on the possibility of using Wiki style software for Genome re-annotation, but nobody has actually created a wiki-based system for genome reannotation (see the recent <a href="http://genomebiology.com/2007/8/1/102">paper </a>in genome Biology by Steven Salzberg). GenomeWiki would be one of the many Wiki re-annotation servers that<br /><br />The last few days have been quite busy for us giving the finishing touches to the website and we have unveiled our logo.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghop21_v7ApKO2427ojeu3O4WUgkkBL_kchKSsAMLNA4loa1FZoj4ZMlriHP-jgqM3EAtP8CMRwb9Yos5gJZdNGvnK6zoY5ugPN6T4kfybMFUpbgin2P4RKQoWNXHekVFtF6cJAZdBlYRI/s1600-h/genomewiki_zebrafish.gif"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghop21_v7ApKO2427ojeu3O4WUgkkBL_kchKSsAMLNA4loa1FZoj4ZMlriHP-jgqM3EAtP8CMRwb9Yos5gJZdNGvnK6zoY5ugPN6T4kfybMFUpbgin2P4RKQoWNXHekVFtF6cJAZdBlYRI/s400/genomewiki_zebrafish.gif" alt="" id="BLOGGER_PHOTO_ID_5210905071115750546" border="0" /></a><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />You should be getting more details on the project at the <a href="http://www.union.wisc.edu/zebrafish/index.html">Madison Meeting</a>.<br />Watch the website for more updates.<br /><br /><br /><br /><br /><br /><a href="javascript:void(0)" tabindex="10" onclick="return false;"><span></span></a><br /><a href="http://miracle.igib.res.in/fishwiki"></a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-14708189110501986542008-06-04T01:51:00.001-07:002008-06-04T01:55:17.713-07:00Meet us at Madison<a href="http://www.union.wisc.edu/zebrafish/index.html"><img src="https://wisccharge.wisc.edu/union/zebrafish2008/images/logo.gif" border="0" /></a><br /><br />See website <a href="http://www.union.wisc.edu/zebrafish/index.html">http://www.union.wisc.edu/zebrafish/index.html</a> for more details<br />See list of participants <a href="https://wisccharge.wisc.edu/union/zebrafish2008/reg_report.asp">here</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-74609036086865702702008-06-04T01:45:00.001-07:002008-06-04T01:49:34.939-07:00FishMap team designs the ZEBRAFISH cover<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5uea6NmtmXIvJD4wkDtnsrKzsVCaUG_1tAMq7aXRITKH2MA8h3OrWuFhiE-Fj-IJjGMbOh8xfS6TtrBc15sZlCPisjTEmmfR3D6HXXU4Ig3itOXHQ_SeFFPgpIYHfOGeWxubEMrRuPBrG/s1600-h/Picture1.png"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5uea6NmtmXIvJD4wkDtnsrKzsVCaUG_1tAMq7aXRITKH2MA8h3OrWuFhiE-Fj-IJjGMbOh8xfS6TtrBc15sZlCPisjTEmmfR3D6HXXU4Ig3itOXHQ_SeFFPgpIYHfOGeWxubEMrRuPBrG/s200/Picture1.png" alt="" id="BLOGGER_PHOTO_ID_5207944902722041330" border="0" /></a>The June issue of Zebrafish featuring FishMap would come up with a brand new cover designed by <a href="http://sites.google.com/a/rnabiology.org/vaibhav/">Vaibhav Jadhav</a>.<br /><br />Thanks to all who hacked into their image collections and handed him over hundreds of images.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-65109344430739158032008-05-28T21:07:00.000-07:002008-05-28T21:13:48.064-07:00FishMap accepted in ZebrafishWe had a wonderful time yesterday after the FishMap manuscript was accepted. And we plan to enjoy this weekend together with our entire team that made this happen.<br /><br />We had a nice time with comments and suggestions from the members of the community and the anonymous reviewers of our paper which significantly enriched the resource.<br /><br />Thank you all for your support!<br /><br />For all of you who would use this tool, please go ahead and cite us as:<br /><br /><pre style="font-family: trebuchet ms,sans-serif; color: rgb(11, 83, 148);"><span><span><span><span style="font-size:85%;">Meli R, Prasad A, Patowary A, Lalwani MK, Maini MK, Sharma M, Singh AR, Kumar G,<br />Jadhav V, Scaria V, Sivasubbu S.<br /><b>FishMap: A community resource for Zebrafish genomics. </b><br /><i>Zebrafish 2008 (In press)</i></span></span></span></span></pre><br />We would be back soon with more updates on datasets.<br /><br />VSUnknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-81243961344023680712008-05-25T01:36:00.000-07:002008-05-25T01:38:32.075-07:00FishMap has new URL<img src="file:///C:/DOCUME%7E1/vinods/LOCALS%7E1/Temp/moz-screenshot-1.jpg" alt="" />FishMap has a new URL. The resource can now me accessed at<br />URL: <a href="http://fishmap.igib.res.in">http://fishmap.igib.res.in</a><br /><br />The old URL <a href="http://miracle.igib.res.in/fishmap">http://miracle.igib.res.in/fishmap</a> would also be accessible for quite some time.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-89748384553962863492008-05-24T08:03:00.000-07:002008-05-24T08:08:45.244-07:00BLAST server added to tool kitFishMap has a BLAST <span style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(68, 68, 68);">server for sequence homology search and a gene ID converter added to its tool kit.<br /></span>SSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-11505769909631318482008-05-11T15:32:00.000-07:002008-05-13T23:33:45.933-07:0050 and moreFishMap today uploaded its 50th track. The data has been pouring from all over, and the FishMap team @ IGIB has been working hard to put it online. We have been currently working on the insertion datasets from various labs. Within a few weeks, you should be updated with these tracks.<br /><b><span style="font-family:Verdana;font-size:85%;"><br />TRACKS READY FOR UPLOAD</span></b><span style="font-family:Verdana;font-size:85%;"><!--webbot bot="Timestamp" S-Type="EDITED" S-Format="%m/%d/%Y" startspan --><!--webbot bot="Timestamp" endspan i-checksum="12542" --> [05/12/2008]</span><ul type="square"><li><span style="font-family:Verdana;font-size:85%;">Becker Lab Insertions </span></li><li><span style="font-family:Verdana;font-size:85%;">Ekker Lab Insertions</span></li><li><span style="font-family:Verdana;font-size:85%;">Hopkins Lab Insertions </span></li><li><span style="font-family:Verdana;font-size:85%;">Kawakami Lab Insertions</span></li><li><span style="font-family:Verdana;font-size:85%;">Korzh Lab Insertions</span></li><li><span style="font-family:Verdana;font-size:85%;">Parinov Lab Insertions</span></li><li><span style="font-family:Verdana;font-size:85%;">Johnson Lab Insertions</span></li></ul>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-18027485251085746032008-04-22T08:15:00.000-07:002008-04-22T08:19:17.852-07:00<span style="font-family:Verdana;font-size:85%;color:#2f5575;">FishMap updates-<br /><br />FishMap currently hosts over 40 datasets (tracks) pertaining to genome-scale data on Zebrafish.<br />You can now suggest your favorite genomic track for inclusion in FishMap!!<br /><br />SSB<br /></span>SSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com0tag:blogger.com,1999:blog-6541892555327735637.post-13853655399606262652008-04-21T23:10:00.000-07:002008-05-13T23:34:44.567-07:00Welcome to FishMap -a community resource for annotation of the zebrafish genome.<br /><br />FishMap incorporates a number of tools and resources such as<br /><br />FishMap Gbrowse - Genome Browser for Zebrafish Genomics datasets.<br />FishMap BLAT - A public BLAT server has been incorporated to FishMap to aid researchers map their sequence of interest to the Zebrafish Genome.<br />FishMap ID converter -Converts Zebrafish GeneIDs commonly used for Zebrafish.<br /><br />FishMap is currently accepting submissions of genome-scale data to be incorporated in the database. Genome-scale predictions are also welcome if the tool/algorithm is published in a peer-reviewed journal. For more information and submissions, please send mail to Dr. Vinod Scaria (vinods@igib.res.in) or Dr. Sridhar Sivasubbu (s.sivasubbu@igib.res.in).<br /><br />The website is currently under construction and will be functional shortly.<br /><br />Good luck<br />SridharSSBhttp://www.blogger.com/profile/00038828386611929725noreply@blogger.com0