>----Mensaje original---- >De: [EMAIL PROTECTED] >Fecha: 27/09/2006 17:13 >Para: <[email protected]> >Asunto: Artemis-users Digest, Vol 12, Issue 1 > >Send Artemis-users mailing list submissions to > [email protected] > >To subscribe or unsubscribe via the World Wide Web, visit > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach the person managing the list at > [EMAIL PROTECTED] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Artemis-users digest..." > > >Today's Topics: > > 1. query on Parallelization --- ACT (Mangala) > 2. Re: query on Parallelization --- ACT (Tim Carver) > 3. Re: Artemis/Database connectivity (Kim Rutherford) > 4. Re: query on Parallelization --- ACT (Mangala) > 5. CHADO connectivity (PIRA (Preethi Ramaiya)) > 6. Re: CHADO connectivity (Tim Carver) > 7. MAGPIE .. artemis (PIRA (Preethi Ramaiya)) > 8. Another genome annotation tool. (Chris Upton) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 1 Sep 2006 16:42:47 +0530 >From: Mangala <[EMAIL PROTECTED]> >Subject: [Artemis-users] query on Parallelization --- ACT >To: [email protected] >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="iso-8859-1" > >Hi, > >Plz anyone clarify me the following questions: > >1. Is the ACT app parallelized? If so, please summarize (in a sentence or >two). If the app uses a DRM, which one - Grid Engine? Something from , > DataSynapse? or Platform? > >2. Whar are the Standards or Technologies used (For example, RMI, MPI, >DRMMA, etc.) ? > >Thanx in advance, >Mangala.k >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://lists.sanger.ac.uk/pipermail/artemis- users/attachments/20060901/5d30b0ac/attachment.html > >------------------------------ > >Message: 2 >Date: Fri, 01 Sep 2006 13:44:20 +0100 >From: Tim Carver <[EMAIL PROTECTED]> >Subject: Re: [Artemis-users] query on Parallelization --- ACT >To: Mangala <[EMAIL PROTECTED]>, <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="us-ascii" > >Hi Mangala > >ACT is a Java application. As a GUI application it does use multi- threading >to spawn separate applications. > >The main standards and technologies are Java. However there are other >technologies it uses, e.g. j2ssh to provide SSH connections. > >Please let me know if you have other specific questions or want to know >more. It may also be good to know where your interests are with ACT. > >Regards >Tim Carver > >On 1/9/06 12:12, "Mangala" <[EMAIL PROTECTED]> wrote: > >> Hi, >> >> Plz anyone clarify me the following questions: >> >> 1. Is the ACT app parallelized? If so, please summarize (in a sentence or >> two). If the app uses a DRM, which one - Grid Engine? Something from , >> DataSynapse? or Platform? >> >> 2. Whar are the Standards or Technologies used (For example, RMI, MPI, DRMMA, >> etc.) ? >> >> Thanx in advance, >> Mangala.k >> >> >> >> >> _______________________________________________ >> Artemis-users mailing list >> [email protected] >> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://lists.sanger.ac.uk/pipermail/artemis- users/attachments/20060901/6c90c89b/attachment.htm > >------------------------------ > >Message: 3 >Date: Fri, 1 Sep 2006 13:58:15 +0100 >From: Kim Rutherford <[EMAIL PROTECTED]> >Subject: Re: [Artemis-users] Artemis/Database connectivity >To: Andrew Stewart <[EMAIL PROTECTED]> >Cc: [email protected] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=us-ascii > >On Thu, 31 Aug 2006 11:34:09 -0400, Andrew Stewart wrote: > >> I'm looking to use Artemis as an interactive front end to a BioSQL or >> Bio::DB::GFF database. I'm aware that Tim Carver is developing >> interaction with Chado, but I was wondering if anyone is aware of any >> other efforts to connect Artemis up with other schemas. I have dug >> up some references to such being done in old mail-list archives I >> googled. > >Some work has been done on Artemis to allow it to use BioJava as a >back-end. As far as I know it's read-only and isn't well tested yet. >I believe BioJava can connect to BioSQL databases so it may be possible >to use BioJava as a bridge between Artemis and BioSQL > >As an example, I think this works in the current Artemis: > art -biojava org.biojava.bio.seq.io.EmblLikeFormat foo.embl > >Kim. > > > >------------------------------ > >Message: 4 >Date: Tue, 5 Sep 2006 10:38:47 +0530 >From: Mangala <[EMAIL PROTECTED]> >Subject: Re: [Artemis-users] query on Parallelization --- ACT >To: "Tim Carver" <[EMAIL PROTECTED]> >Cc: [email protected] >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="iso-8859-1" > >Hi Tim, > >Thanx for ur info. > >Sun Microsystems Inc. is currently evaluating ACT as part of its >initiatives in the space of open source applications. While I'm unable to >go into the specifics of this project at this stage, the upshot is that >it'll vastly extend the reach of your application to a much wider audience. > > >To help us with the initial evaluation, could you please answer the >following questions? > >1. Since it does support multi-threading, we can make it parallelized. But Is >the application currently parallelized? If so, what technologies it uses for >to make it parallelized like for ex: RMI, MPI, DRMMA, PVM etc. > >2. What is the approximate size of the user community for this application? >ie the approximate no of users for ACT. > >Your cooperation is appreciated. > >Reagrds, >Mangala.k > > >On 9/1/06, Tim Carver <[EMAIL PROTECTED]> wrote: >> >> Hi Mangala >> >> ACT is a Java application. As a GUI application it does use >> multi-threading to spawn separate applications. >> >> The main standards and technologies are Java. However there are other >> technologies it uses, e.g. j2ssh to provide SSH connections. >> >> Please let me know if you have other specific questions or want to know >> more. It may also be good to know where your interests are with ACT. >> >> Regards >> Tim Carver >> >> >> On 1/9/06 12:12, "Mangala" <[EMAIL PROTECTED]> wrote: >> >> Hi, >> >> Plz anyone clarify me the following questions: >> >> 1. Is the ACT app parallelized? If so, please summarize (in a sentence or >> two). If the app uses a DRM, which one - Grid Engine? Something from , >> DataSynapse? or Platform? >> >> 2. Whar are the Standards or Technologies used (For example, RMI, MPI, >> DRMMA, etc.) ? >> >> Thanx in advance, >> Mangala.k >> >> >> >> ------------------------------ >> _______________________________________________ >> Artemis-users mailing list >> [email protected] >> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://lists.sanger.ac.uk/pipermail/artemis- users/attachments/20060905/617b4c8b/attachment-0001.html > >------------------------------ > >Message: 5 >Date: Tue, 19 Sep 2006 11:38:26 -0700 >From: "PIRA \(Preethi Ramaiya\)" <[EMAIL PROTECTED]> >Subject: [Artemis-users] CHADO connectivity >To: <[email protected]> >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="us-ascii" > >Hi > >I am following up on a post I made in Jan 2006. I am currently trying to >use Artemis8 and GFF3. We are planning on using the CHADO schema from >GMOD and also, Gbrowse. We have the CHADO/Gbrowse part working with some >test GFF3 data that we have adapted from the Artemis GFF3 dump. Is there >any plan to get CHADO connectivity in Artemis soon..? :-) That might >save us an Artemis->Apollo migration. We like the user interface in >Artemis (bacterial genomes) and would like to have a straight pipe into >CHADO. > >Thank you! >Regards >Preethi >------------------------------------------------------------------------ >----- > >"Hi Preethi > >I plan to get a Artemis/ACT release out in the next couple of months >(hopefully sooner than later). To get it talking to CHADO it has become >more >GFF3 compliant which is what we are working towards but this has not >been >used in anger yet. > >Regards >Tim" > > > > >------------------------------ > >Message: 6 >Date: Mon, 25 Sep 2006 10:22:57 +0100 >From: Tim Carver <[EMAIL PROTECTED]> >Subject: Re: [Artemis-users] CHADO connectivity >To: "PIRA (Preethi Ramaiya)" <[EMAIL PROTECTED]>, > <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="US-ASCII" > >Hi Preethi > >This is still work in progress. However, I have Artemis reading and writing >to a test CHADO database (using either iBatis or straight JDBC) and we have >been working on the java interface to do this. This is top priority on my >list of things to do over the next few months. If you want to try out what >it currently supports you can get the development version and I can provide >more information on how to get it talking to a database. > >Regards >Tim > > >On 19/9/06 19:38, "PIRA (Preethi Ramaiya)" <[EMAIL PROTECTED]> wrote: > >> Hi >> >> I am following up on a post I made in Jan 2006. I am currently trying to >> use Artemis8 and GFF3. We are planning on using the CHADO schema from >> GMOD and also, Gbrowse. We have the CHADO/Gbrowse part working with some >> test GFF3 data that we have adapted from the Artemis GFF3 dump. Is there >> any plan to get CHADO connectivity in Artemis soon..? :-) That might >> save us an Artemis->Apollo migration. We like the user interface in >> Artemis (bacterial genomes) and would like to have a straight pipe into >> CHADO. >> >> Thank you! >> Regards >> Preethi >> ------------------------------------------------------------------------ >> ----- >> >> "Hi Preethi >> >> I plan to get a Artemis/ACT release out in the next couple of months >> (hopefully sooner than later). To get it talking to CHADO it has become >> more >> GFF3 compliant which is what we are working towards but this has not >> been >> used in anger yet. >> >> Regards >> Tim" >> >> >> _______________________________________________ >> Artemis-users mailing list >> [email protected] >> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > > > > > >------------------------------ > >Message: 7 >Date: Wed, 27 Sep 2006 12:46:09 -0700 >From: "PIRA \(Preethi Ramaiya\)" <[EMAIL PROTECTED]> >Subject: [Artemis-users] MAGPIE .. artemis >To: <[email protected]> >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="us-ascii" > >Hi > >Has anyone tried out the MAGPIE/bluejay system out of >http://magpie.ucalgary.edu and compared ease of use/feature sets with >artemis (web-based) or apollo -based system for annotating microbial >genomes. I am interested in your experiences and what your conclusions >were. > >Specifically for a community based annotation effort where it will be >necessary for third party editing of things like gene-names, functions >etc but not necessarily of sequence data itself. > > >Preethi > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://lists.sanger.ac.uk/pipermail/artemis- users/attachments/20060927/6b9ccc16/attachment-0001.htm > >------------------------------ > >Message: 8 >Date: Wed, 27 Sep 2006 13:10:58 -0700 >From: Chris Upton <[EMAIL PROTECTED]> >Subject: [Artemis-users] Another genome annotation tool. >To: [email protected] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="us-ascii" > >Hi, >I thought this might be a good place to advertise our new tool: >Genome Annotation Transfer Utility (GATU) > >We developed it because we found ourselves annotating lots of viral >genomes for which there was a close relative already annotated (eg >SARS). Our paper (below) also describes results using it on >bacterial genomes. > >Essentially, GATU takes the proteins/mature peptides of the reference >genome and BLASTs against the genome to be annotated in order to find >already known genes. It also finds novel ORFs, unique in the target >genome - and allows further analysis. >It's not a gene predictor, but we've found that it can annotate >90% >of genes without intervention and allows the user to keep control >over selection of genes to be annotated. >The end product is a GenBank file. > >See: >http://athena.bioc.uvic.ca/workbench.php?tool=gatu&db= > >Tcherepanov VT, Ehlers A, Upton C. (2006) Genome Annotation Transfer >Utility (GATU): Rapid annotation of viral genomes using a closely >related reference genome. BMC Genomics. 2006 Jun 13;7(1):150 >http://www.biomedcentral.com/1471-2164/7/150/abstract > >Questions welcome! > >Also check out http://www.biodirectory.com/uptons_blog.html > >Chris Upton > >Biochemistry and Microbiology Tel. 250-721-6507 >University of Victoria Fax 250-721- 8855 >P.O. Box 3055 STN CSC >Victoria, BC V8W 3P6 >Canada > >web.uvic.ca/~cupton >www.virology.ca >http://www.biodirectory.com/uptons_blog.html > > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://lists.sanger.ac.uk/pipermail/artemis- users/attachments/20060927/bf2c6246/attachment.html > >------------------------------ > >_______________________________________________ >Artemis-users mailing list >[email protected] >http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > >End of Artemis-users Digest, Vol 12, Issue 1 >******************************************** >
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