From xenopus at mbl.edu Wed Oct 1 08:49:17 2014 From: xenopus at mbl.edu (National Xenopus Resource) Date: Wed, 1 Oct 2014 08:49:17 -0400 (EDT) Subject: [Xenopus] Thank you-Xenopus mutation grant In-Reply-To: <999285026.1116693.1412167346977.JavaMail.zimbra@mbl.edu> Message-ID: <478867662.1117485.1412167757193.JavaMail.zimbra@mbl.edu> Dear Xenopus community, Thank you to everyone who sent in letters of support and/or filled out the Xenopus Mutant Survey in response to my emails. I received many more letters of support and responses than I expected, and more than enough to write the grant. I am happy to say that I have submitted an R01 to the Xenopus PAR to make 100-200 mutants for the community. If this grant is funded we can then begin making these mutants for the community. This project is for the community so when we start working on it we will contact each individual who responded to the Mutant survey to discuss plans for the specific mutant requested. The goal is to interact with each of you to identify the targeted region. Our hope is that we can make over 30 mutant lines each year. Once again I would like to thank each of you for your support in this project and I look forward to working with you on making these mutant lines. Sincerely, Marko Horb --------------------------------------------------------------------------------------- Marko Horb, Ph.D. Director, National Xenopus Resource (NXR) Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543 Email: xenopus at mbl.edu Office: 508-289-7627 Cell: 508-564-3764 http://www.mbl.edu/xenopus https://twitter.com/xenopusnxr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mbl.edu/pipermail/xenopus/attachments/20141001/2c372f2f/attachment.html From xenopus at mbl.edu Sat Oct 11 13:17:49 2014 From: xenopus at mbl.edu (National Xenopus Resource) Date: Sat, 11 Oct 2014 13:17:49 -0400 (EDT) Subject: [Xenopus] Last Chance- Genome Editing Workshop In-Reply-To: <2107333601.1846498.1413047625057.JavaMail.zimbra@mbl.edu> Message-ID: <145111093.1846568.1413047869032.JavaMail.zimbra@mbl.edu> Hello Xenopus Community A final reminder to register for the upcoming Genome Editing Workshop. We still have several places available. Registration will close Friday October 17th. So far it looks like a great group for the first genome editing workshop. Lots will be learned and it will be an enjoyable time. Remember the fee for each registrant includes one custom mutant line to be grown at the NXR for you. That's not a bad deal considering the cost also includes a week long workshop and that includes all room and board. http://www.mbl.edu/xenopus/workshops/genomeediting-workshop If you have any questions do not hesitate to ask. The syllabus is also available on the web page. Marko --------------------------------------------------------------------------------------- Marko Horb, Ph.D. Director, National Xenopus Resource (NXR) Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543 Email: xenopus at mbl.edu Office: 508-289-7627 Cell: 508-564-3764 http://www.mbl.edu/xenopus https://twitter.com/xenopusnxr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mbl.edu/pipermail/xenopus/attachments/20141011/48415ec6/attachment.html From walentek at berkeley.edu Wed Oct 29 22:09:33 2014 From: walentek at berkeley.edu (Peter Walentek) Date: Wed, 29 Oct 2014 19:09:33 -0700 Subject: [Xenopus] Xenopus genome blast Message-ID: Hi everyone, the Xenopus genome blast function does not work for me for a while now. Every now and then I can blast something, but most of the time the search doesn't start or gives me an immediate error. Tried different browsers/computers and other people had the same problem. Does anyone know what is going on and when blast will be fully functional again? Thanks a lot! Peter -- Dr. Peter Walentek Harland Lab Dept. Molecular & Cell Biology University of California at Berkeley walentek at berkeley.edu From asuzuki at hiroshima-u.ac.jp Thu Oct 30 00:42:31 2014 From: asuzuki at hiroshima-u.ac.jp (Atsushi Suzuki) Date: Thu, 30 Oct 2014 13:42:31 +0900 Subject: [Xenopus] Xenopus genome blast In-Reply-To: References: Message-ID: Hi Peter, I have just tested Xenbase BLAST against both X. laevis v7 and X. tropicalis v8. Both of them worked properly using Google Chrome. You might want to try Japanese site at National Institute of Genetics. http://xenopus.lab.nig.ac.jp/ Best, Atsushi ------------------------------------------------------------------- Atsushi Suzuki, Ph.D. Associate Professor Institute for Amphibian Biology Hiroshima University Graduate School of Science Kagamiyama 1-3-1, Higashihiroshima 739-8526 JAPAN TEL: 81-824-24-7103 e-mail: asuzuki at hiroshima-u.ac.jp ----------------------------------------------------------------- ________________________________________ From: Peter Walentek [mailto:walentek at berkeley.edu] Sent: Thursday, October 30, 2014 1:07 PM To: Atsushi Suzuki Subject: Re: [Xenopus] Xenopus genome blast Dear Atsushi,? I meant the one on Xenbase, for blasting against laevis genome assembly.? Thanks a lot for your response. Peter Am 29.10.2014, 20:56 Uhr, schrieb Atsushi Suzuki : Dear Peter, ? It seems to be working at least, in my hand (not a Trick). ? Is this the page that you are using? ? Xenopus (Silurana) tropicalis (western clawed frog) Nucleotide BLAST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC =OGP__8364__10706 ? Best wishes, ? Atsushi ? ------------------------------------------------------------------- Atsushi Suzuki, Ph.D. Associate Professor Institute for Amphibian Biology Hiroshima University Graduate School of Science Kagamiyama 1-3-1, Higashihiroshima 739-8526 JAPAN TEL: 81-824-24-7103 e-mail: asuzuki at hiroshima-u.ac.jp ----------------------------------------------------------------- ? ? ? ? > -----Original Message----- > From: xenopus-bounces at lists.mbl.edu [mailto:xenopus-bounces at lists.mbl.edu] > On Behalf Of Peter Walentek > Sent: Thursday, October 30, 2014 11:10 AM > To: xenopus at lists.mbl.edu > Subject: [Xenopus] Xenopus genome blast > > Hi everyone, > > the Xenopus genome blast function does not work for me for a while now. > Every now and then I can blast something, but most of the time the search > doesn't start or gives me an immediate error. Tried different > browsers/computers and other people had the same problem. > > Does anyone know what is going on and when blast will be fully functional > again? > > Thanks a lot! > Peter > > -- > Dr. Peter Walentek > Harland Lab > Dept. Molecular & Cell Biology > University of California at Berkeley > > walentek at berkeley.edu > _______________________________________________ > Xenopus mailing list > Xenopus at lists.mbl.edu > https://lists.mbl.edu/mailman/listinfo/xenopus -- Dr. Peter Walentek Harland Lab Dept. Molecular & Cell Biology University of California at Berkeley walentek at berkeley.edu From ilblitz at uci.edu Thu Oct 30 01:25:14 2014 From: ilblitz at uci.edu (Ira Blitz) Date: Wed, 29 Oct 2014 22:25:14 -0700 Subject: [Xenopus] Xenopus genome blast In-Reply-To: References: Message-ID: <05FA7C0B-3B56-4583-A1BB-E4760E3C5F4C@uci.edu> I used Xenbase blast to search both tropicalis and laevis v8 and 7 respectively one minute ago and they work for me (using Firefox). > On Oct 29, 2014, at 9:42 PM, Atsushi Suzuki wrote: > > Hi Peter, > > I have just tested Xenbase BLAST against both X. laevis v7 and X. tropicalis > v8. > Both of them worked properly using Google Chrome. > > You might want to try Japanese site at National Institute of Genetics. > http://xenopus.lab.nig.ac.jp/ > > Best, > > Atsushi > > ------------------------------------------------------------------- > Atsushi Suzuki, Ph.D. > Associate Professor > Institute for Amphibian Biology > Hiroshima University Graduate School of Science Kagamiyama 1-3-1, > Higashihiroshima 739-8526 JAPAN > TEL: 81-824-24-7103 > e-mail: asuzuki at hiroshima-u.ac.jp > ----------------------------------------------------------------- > ________________________________________ > From: Peter Walentek [mailto:walentek at berkeley.edu] > Sent: Thursday, October 30, 2014 1:07 PM > To: Atsushi Suzuki > Subject: Re: [Xenopus] Xenopus genome blast > > Dear Atsushi, > > I meant the one on Xenbase, for blasting against laevis genome assembly. > > Thanks a lot for your response. > > Peter > > > Am 29.10.2014, 20:56 Uhr, schrieb Atsushi Suzuki > : > > > Dear Peter, > > It seems to be working at least, in my hand (not a Trick). > > Is this the page that you are using? > > Xenopus (Silurana) tropicalis (western clawed frog) Nucleotide BLAST > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC > =OGP__8364__10706 > > Best wishes, > > Atsushi > > ------------------------------------------------------------------- > Atsushi Suzuki, Ph.D. > Associate Professor > Institute for Amphibian Biology > Hiroshima University Graduate School of Science Kagamiyama 1-3-1, > Higashihiroshima 739-8526 JAPAN > TEL: 81-824-24-7103 > e-mail: asuzuki at hiroshima-u.ac.jp > ----------------------------------------------------------------- > > > > > >> -----Original Message----- >> From: xenopus-bounces at lists.mbl.edu [mailto:xenopus-bounces at lists.mbl.edu] >> On Behalf Of Peter Walentek >> Sent: Thursday, October 30, 2014 11:10 AM >> To: xenopus at lists.mbl.edu >> Subject: [Xenopus] Xenopus genome blast >> >> Hi everyone, >> >> the Xenopus genome blast function does not work for me for a while now. >> Every now and then I can blast something, but most of the time the search >> doesn't start or gives me an immediate error. Tried different >> browsers/computers and other people had the same problem. >> >> Does anyone know what is going on and when blast will be fully functional >> again? >> >> Thanks a lot! >> Peter >> >> -- >> Dr. Peter Walentek >> Harland Lab >> Dept. Molecular & Cell Biology >> University of California at Berkeley >> >> walentek at berkeley.edu >> _______________________________________________ >> Xenopus mailing list >> Xenopus at lists.mbl.edu >> https://lists.mbl.edu/mailman/listinfo/xenopus > > > -- > Dr. Peter Walentek > Harland Lab > Dept. Molecular & Cell Biology > University of California at Berkeley > > walentek at berkeley.edu > > > _______________________________________________ > Xenopus mailing list > Xenopus at lists.mbl.edu > https://lists.mbl.edu/mailman/listinfo/xenopus > From webb at ncbi.nlm.nih.gov Thu Oct 30 13:36:18 2014 From: webb at ncbi.nlm.nih.gov (Webb, David (NIH/NLM/NCBI) [C]) Date: Thu, 30 Oct 2014 17:36:18 +0000 Subject: [Xenopus] Xenopus genome blast In-Reply-To: References: Message-ID: <0EEB1C58BAFB5048958ED3CC74FEA73D0F12E44F@MLBXV09.nih.gov> Hi everyone, It appears to have been a temporary server problem at NCBI as I haven't been able to reproduce the problem. If similar problems happen in the future you may use the "help" tab near the top of the Xenopus BLAST page to send a message to blast-help at ncbi.nlm.nih.gov or you may send an e-mail to me if you have additional questions or concerns about Xenopus resources at NCBI. Part of my job at NCBI is to act as a liaison between the Xenopus research community and the software and database developers at NCBI. I welcome your emails as it enables NCBI to improve the resources we offer to our most frequent users - the research community. Best wishes, David David M. Webb, Ph.D. Staff Scientist Reference Sequence Project NCBI/NLM/NIH Besthesda, MD., U.S.A. webb at ncbi.nlm.nih.gov Phone #: 301.402.8705 -----Original Message----- From: Peter Walentek [mailto:walentek at berkeley.edu] Sent: Wednesday, October 29, 2014 10:10 PM To: xenopus at lists.mbl.edu Subject: [Xenopus] Xenopus genome blast Hi everyone, the Xenopus genome blast function does not work for me for a while now. Every now and then I can blast something, but most of the time the search doesn't start or gives me an immediate error. Tried different browsers/computers and other people had the same problem. Does anyone know what is going on and when blast will be fully functional again? Thanks a lot! Peter -- Dr. Peter Walentek Harland Lab Dept. Molecular & Cell Biology University of California at Berkeley walentek at berkeley.edu _______________________________________________ Xenopus mailing list Xenopus at lists.mbl.edu https://lists.mbl.edu/mailman/listinfo/xenopus From xenbase at ucalgary.ca Thu Oct 30 14:52:21 2014 From: xenbase at ucalgary.ca (xenbase) Date: Thu, 30 Oct 2014 14:52:21 -0400 Subject: [Xenopus] Xenbase Fall 2014 Newsletter Message-ID: Xenbase Fall 2014 Newsletter Highlights of the new Xenbase v3.3 Morpholinos have launched on Xenbase!! Morpholino antisense oligos (MOs) are widely used in Xenopus to suppress gene function. Xenbase has introduced a comprehensive catalog of ~1585 published MOs so researchers can quickly identify effective Xenopus specific reagents. Access the new MO database from Xenbase menus and front page MOs are mapped to genome and can be viewed on GBrowse Search MOs via gene symbol, sequence or name used in the publication Each MO has a dedicated page, showing its alignment to genome (see e.g. Nodal5.2 MO2) Target/Off Target hits illustrated MOs are listed as reagents at bottom on gene page MOs used in publications are listed on article?s Xenbase page. New MOs will be added as articles are published and curated. Genome Builds & Gene Models: Latest Updates from JGI & Adam Sessions (Rokhsar Group) X. laevis v7.2 annotation/gene model is now shown on the v7.1 genome build on GBrowse X. laevis L and S (long and short) genomes now on GBrowse We are working on reconciling X. laevis L & S alleles on gene pages X. tropicalis genome build v8.0 has more gene names assigned on GBrowse GBrowse snapshots are bigger and crisper on gene pages Human Disease Associations: Single-gene disease associations are now on ~14,600 gene pages, facilitating direct comparison of information from Xenopus genes with their human orthologs (e.g. tgfb1). Diseases can be searched using OMIM ID from the main search menu. HomoloGene: New HomoloGene link is on ?Genes? tile of the Xenbase front page. This link goes directly to a Xenopus search of this NCBI resource that helps construct putative homology groups from the complete gene sets of a wide range of eukaryotic species. Transgenes Naming Guidelines: Xenbase has drafted the ?Xenopus Transgenic Nomenclature Guidelines? in consultation with the NXR, EXRC and NBRP, and gene nomenclature committee. These guidelines are based on the well-established rules for zebrafish and mouse, with the goal of increasing experimental reproducibility and data clarity cross model organisms. Authors are strongly encouraged to follow the guidelines when naming transgenes or mutant or transgenic Xenopus lines. Contact Xenbase (xenbase at ucalgary.ca) with comments/questions and for help naming your constructs. See http://www.xenbase.org/gene/static/tgNomenclature.jsp Coming Soon: Xenbase Forums A discussion forum/community bulletin board to discuss and ask advice on all aspects of Xenopus research (e.g., experimental design & data analysis for ChipSeq, RNASeq, Morpholinos, ISH, genes etc.). More details of the recent updates to Xenbase are detailed in Karpinka et al (2014). Xenbase, the Xenopus Model Organism Database; new virtualized system, data types and genomes. Nucl. Acids Res. first published online October 13, 2014 doi:10.1093/nar/gku956 http://nar.oxfordjournals.org/content/early/2014/10/13/nar.gku956.full?sid=e82f949b-5e2a-4933-ab1e-d39051c74116 Image or Data Submissions? Questions or Comments? Contact us at xenbase at ucalgary.ca http://www.xenbase.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mbl.edu/pipermail/xenopus/attachments/20141030/3e089897/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 3612 bytes Desc: not available Url : http://lists.mbl.edu/pipermail/xenopus/attachments/20141030/3e089897/attachment-0001.png