From simont at hmgc.mcw.edu Mon Aug 13 13:13:28 2007 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Mon Aug 13 13:15:41 2007 Subject: [rat-forum] Pathway tools and data in Apropos Message-ID: Dear List, We've released an updated screencast detailing the current resources we have for Rat, Mouse and Human Pathways as part of the Apropos data annotation tool. You can find the screencast here: http://apropos.rubyforge.org/Apropos%20Annotation%20Platform/ VC_KeggPathways.html While pathways aren't the primary focus of the Apropos database it does have some useful genome-oriented views of the pathways that may be of use to people working with QTLs or consomic/congenic strains * View the genes involved in a given KEGG pathway and see an image of their genome locations in Rat, Mouse and Human. * Find pathways on a particular Rat, Mouse or Human Chromosome * Quick access to basic literature search results for a given pathway I'd be interested in any other ideas for pathway-oriented searches that people might have, eg. * Find pathways in a specific region (eg. get a list of pathways on Rat Chr 2 between 1234567bp and 4567890 bp) * Find and compare pathways in multiple regions and/or in multiple species - would be useful to see if any pathways are in common between QTL regions within and between species. * Show any phenotypes associated with proteins in a given particular pathway I'd love to hear any comments on what we have so far, plus any other thoughts for pathway-oriented reports/searches that people would like to have so we can keep the tool evolving in the right direction. Best, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From jdepons at mcw.edu Tue Aug 14 15:27:00 2007 From: jdepons at mcw.edu (De Pons, Jeff) Date: Tue Aug 14 15:26:28 2007 Subject: [rat-forum] RGD Survey Question Of The Week Message-ID: <1448A38A42714048B9C53E473E13CCF0011F961C@davis.hmgc.mcw.edu> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 7922 bytes Desc: image002.jpg Url : http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070814/24c37b9d/attachment.jpe From hsarunk at yahoo.com Wed Aug 22 02:49:06 2007 From: hsarunk at yahoo.com (AKHS) Date: Wed Aug 22 08:29:41 2007 Subject: [rat-forum] Information request In-Reply-To: Message-ID: <242273.56868.qm@web30408.mail.mud.yahoo.com> Dear Members of the RCF Can you kindly mail me about the weekly cost involved at your facility to maintain a rat or mice. (kindly exclude the salary coponent of the workers involved in it). Looking forward to hearing from you. Regards Arun ____________________________________________________________________________________ Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 From moisan at bordeaux.inserm.fr Wed Aug 22 09:45:50 2007 From: moisan at bordeaux.inserm.fr (Marie-Pierre Moisan) Date: Wed Aug 22 09:57:50 2007 Subject: [rat-forum] Information request In-Reply-To: <242273.56868.qm@web30408.mail.mud.yahoo.com> References: <242273.56868.qm@web30408.mail.mud.yahoo.com> Message-ID: <46CC4C1E.60707@bordeaux.inserm.fr> AKHS a ?crit : > In our Institute, the cost is roughly 1.20 euros per week per animal > Dear Members of the RCF > > Can you kindly mail me about the weekly cost involved > at your facility to maintain a rat or mice. (kindly > exclude the salary coponent of the workers involved in > it). > > Looking forward to hearing from you. > > Regards > Arun > > > > ____________________________________________________________________________________ > Sick sense of humor? Visit Yahoo! TV's > Comedy with an Edge to see what's on, when. > http://tv.yahoo.com/collections/222 > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > > From mlkal at mcw.edu Wed Aug 22 10:04:27 2007 From: mlkal at mcw.edu (Kaldunski, Mary) Date: Wed Aug 22 10:06:10 2007 Subject: [rat-forum] Information request In-Reply-To: <242273.56868.qm@web30408.mail.mud.yahoo.com> References: <242273.56868.qm@web30408.mail.mud.yahoo.com> Message-ID: <8F78639AC56F4143B267FE5F5A1B92C8CE2F05@guyton.phys.mcw.edu> Per diem alone is currently $2.66 a week per rat, here. It is going to be increased next year, though I haven't seen what the increase will be. Mary Mary L. Kaldunski Program Coordinator Dept of Physiology Medical College of Wisconsin 8701 Watertown Plank Rd. Milwaukee, WI 53226 414-456-8840 fax 414-456-6546 mlkal@mcw.edu -----Original Message----- From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of AKHS Sent: Wednesday, August 22, 2007 2:49 AM To: Rat Community Forum Subject: [rat-forum] Information request Dear Members of the RCF Can you kindly mail me about the weekly cost involved at your facility to maintain a rat or mice. (kindly exclude the salary coponent of the workers involved in it). Looking forward to hearing from you. Regards Arun ________________________________________________________________________ ____________ Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 _______________________________________________ rat-forum mailing list rat-forum@mcw.edu http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum From tordoff at monell.org Wed Aug 22 10:21:28 2007 From: tordoff at monell.org (Michael Tordoff) Date: Wed Aug 22 10:23:24 2007 Subject: [rat-forum] Information request In-Reply-To: <242273.56868.qm@web30408.mail.mud.yahoo.com> References: <242273.56868.qm@web30408.mail.mud.yahoo.com> Message-ID: <008f01c7e4d0$1c81d630$55858290$@org> Arun: You might find useful the list of animal per diems available at http://www.ahc.umn.edu/rar/perdiems_others.html It will be difficult to find rates that do not incorporate the costs of running the animal facility, including workers involved (as you requested), because NIH grants require this to be part of the direct costs of the research project. ________________________________ Michael G. Tordoff, Ph.D. Monell Chemical Senses Center Philadelphia, PA 19104, USA ________________________________ e-mail: tordoff@monell.org phone and fax: (267)-519-4805 web: www.monell.org Monell Mouse Taste Phenotyping Project: web: www.monell.org/MMTPP ________________________________ -----Original Message----- From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of AKHS Sent: Wednesday, August 22, 2007 3:49 AM To: Rat Community Forum Subject: [rat-forum] Information request Dear Members of the RCF Can you kindly mail me about the weekly cost involved at your facility to maintain a rat or mice. (kindly exclude the salary coponent of the workers involved in it). Looking forward to hearing from you. Regards Arun ____________________________________________________________________________ ________ Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 _______________________________________________ rat-forum mailing list rat-forum@mcw.edu http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum __________ NOD32 2475 (20070822) Information __________ This message was checked by NOD32 antivirus system. http://www.eset.com From bcj1 at psu.edu Wed Aug 22 13:43:35 2007 From: bcj1 at psu.edu (Byron C. Jones) Date: Wed Aug 22 14:03:23 2007 Subject: [rat-forum] Information request In-Reply-To: <242273.56868.qm@web30408.mail.mud.yahoo.com> References: <242273.56868.qm@web30408.mail.mud.yahoo.com> Message-ID: <7.0.1.0.2.20070822144207.05664190@psu.edu> Dear Arun, At Penn State, we charge .18 per mouse per day and for rats, .38. Our costs are comprehensive and it would be impossible to break out labor or materials. Best wishes Byron At 03:49 AM 8/22/2007, you wrote: >Dear Members of the RCF > >Can you kindly mail me about the weekly cost involved >at your facility to maintain a rat or mice. (kindly >exclude the salary coponent of the workers involved in >it). > >Looking forward to hearing from you. > >Regards >Arun > > > >____________________________________________________________________________________ >Sick sense of humor? Visit Yahoo! TV's >Comedy with an Edge to see what's on, when. >http://tv.yahoo.com/collections/222 >_______________________________________________ >rat-forum mailing list >rat-forum@mcw.edu >http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum Byron C. Jones, Ph.D. Professor of Biobehavioral Health and Pharmacology Professor-in-Charge of the BBH Graduate Program The Pennsylvania State University 315 East Health and Human Development University Park, PA 16802-6508 (814) 863 0167 (voice) (814) 863 7525 ( FAX) From dongbing75 at hotmail.com Wed Aug 22 18:17:34 2007 From: dongbing75 at hotmail.com (dong bing) Date: Wed Aug 22 18:29:16 2007 Subject: [rat-forum] Isolation of mammary epithelia Message-ID: Hi dear, Could you help me on isolation of mammary gland epithelia cells from other types of cells like adipose cells from rat mammary gland tissue? I need to do Western Blot and real time PCR. Thanks. Bing ************************************************ Bing Dong dongbing75@hotmail.com > From: rat-forum-request@mcw.edu> Subject: rat-forum Digest, Vol 5, Issue 1> To: rat-forum@mcw.edu> Date: Wed, 22 Aug 2007 08:29:51 -0500> > Send rat-forum mailing list submissions to> rat-forum@mcw.edu> > To subscribe or unsubscribe via the World Wide Web, visit> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> or, via email, send a message with subject or body 'help' to> rat-forum-request@mcw.edu> > You can reach the person managing the list at> rat-forum-owner@mcw.edu> > When replying, please edit your Subject line so it is more specific> than "Re: Contents of rat-forum digest..."> > > Rat Community Forum DIGEST of messages> > Today's Topics:> > 1. Apropos - new annotation tool for proteomic and genomic> experiments from MCW Proteomics Center (Twigger Simon)> 2. Pathway tools and data in Apropos (Twigger Simon)> 3. RGD Survey Question Of The Week (De Pons, Jeff)> 4. Information request (AKHS)> > > ----------------------------------------------------------------------> > Message: 1> Date: Mon, 30 Jul 2007 08:32:29 -0500> From: Twigger Simon > Subject: [rat-forum] Apropos - new annotation tool for proteomic and> genomic experiments from MCW Proteomics Center> To: Rat Forum Community > Message-ID: <5187463F-33A8-44B4-B82A-A7003AB9697E@hmgc.mcw.edu>> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed> > Dear List,> > As part of our work at the NHLBI proteomics center at the Medical > College of Wisconsin (http://proteomics.mcw.edu) we have been > developing a new data annotation tool and it is ready for a more > public release. The tool is called Apropos and it combines a > comprehensive list of rat, mouse and human protein data with Gene > Ontology, pathway and phenotype annotations along with mapping data > to provide a three-species annotation database. This enables you to > see orthology relationships between species and functional > annotations from all three species. For example, you can easily view > annotations from mouse and human when studying rat genes/proteins, or > to pull in information about rat and mouse when studying human genes/ > proteins.> > The tool has two main uses: 1) as a personal data annotation tool > where you can create personal account and then upload your lists of > rat, mouse or human genes or proteins from your 'omic experiment and > create an annotation dataset, and 2) as a 3 species annotation > database that you can use to find out information about individual > genes or pathways in Rat, Mouse and Human.> > Apropos is an open source project and more information including > screenshots, screencasts and other details are available from the > project's development site:> > http://apropos.rubyforge.org/> > The main database itself is available here: http://apropos.mcw.edu/> > Example uses include viewing individual protein reports, eg Rat A2m: > http://apropos.mcw.edu/rgd/2004> > KEGG pathways are included with Rat, Mouse and Human genes displayed > on our dynamic flash genome viewer along with links to literature at > Hubmed (a more advanced interface to Pubmed) and Google Scholar.> > Here is the link for Fatty Acid Metabolism: http://apropos.mcw.edu/ > kegg_pathways/show/11> > You can also find pathways that have proteins on a specific > chromosome. For example if you work with consomic animals and want to > know about the pathways on your specific chromosome, or know that > Chromosome 20 in Human is important in your disease study you can > find out which pathways have genes/proteins on Chromosome 20 in Human:> > http://apropos.mcw.edu/kegg_pathways/chromosome_filter? > chromosome=20&taxon_id=9606> > > The current focus of the tool is to provide an annotation environment > that enables you to store and keep track of your various gene/protein > lists and quickly find information out about these genes individually > or in bulk. It was built recognizing that one species doesn't give > the complete picture and so being able to take a Rat gene and find > out about what is known in Human or mouse is an important task. It > doesn't have statistics (eg. GO enrichment, over-representation, etc) > at this point because of the challenges involved in determining the > reference gene set for those analyses. We'd like to implement > something like this in the future once we've worked out the stats > behind this approach. We're very interested in providing ways for you > to compare and contrast protein/gene sets and visualize the results > of those comparisons, eg. compare the known functions and pathways > between a syntenic region in Rat and Human, or compare genes found in > a microarray dataset with those found in a proteomic screen.> > The tool is very much under active development and we welcome your > feedback and suggestions on how it can be improved and made more > useful. Feel free to email me directly (simont@hmgc.mcw.edu) or > perhaps even better, use the project site to send the information in > so we can keep it in one place: we have a 'new feature' tracker that > you can use to submit new feature requests:> http://rubyforge.org/tracker/?func=add&group_id=3573&atid=13751> > It's also entirely likely there are bugs and so we have a bug > tracker, you can submit a new bug report here:> http://rubyforge.org/tracker/?func=add&group_id=3573&atid=13748> > Thank you for having a look at the tool and I hope that it will > provide a useful addition to your data analysis toolbox.> > Best regards,> > Simon.> > --> > Simon N. Twigger, Ph.D.> Assistant Professor, Department of Physiology> Medical College of Wisconsin> 8701 Watertown Plank Road,> Milwaukee, WI, USA> tel: 414-456-8802> fax: 414-456-6595> AIM/iChat: simontatmcw> > > > > ------------------------------> > Message: 2> Date: Mon, 13 Aug 2007 13:13:28 -0500> From: Twigger Simon > Subject: [rat-forum] Pathway tools and data in Apropos> To: Rat Community Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed> > Dear List,> > We've released an updated screencast detailing the current resources > we have for Rat, Mouse and Human Pathways as part of the Apropos data > annotation tool. You can find the screencast here:> > http://apropos.rubyforge.org/Apropos%20Annotation%20Platform/ > VC_KeggPathways.html> > While pathways aren't the primary focus of the Apropos database it > does have some useful genome-oriented views of the pathways that may > be of use to people working with QTLs or consomic/congenic strains> > * View the genes involved in a given KEGG pathway and see an image of > their genome locations in Rat, Mouse and Human.> * Find pathways on a particular Rat, Mouse or Human Chromosome> * Quick access to basic literature search results for a given pathway> > I'd be interested in any other ideas for pathway-oriented searches > that people might have, eg.> > * Find pathways in a specific region (eg. get a list of pathways on > Rat Chr 2 between 1234567bp and 4567890 bp)> * Find and compare pathways in multiple regions and/or in multiple > species - would be useful to see if any pathways are in common > between QTL regions within and between species.> * Show any phenotypes associated with proteins in a given particular > pathway> > I'd love to hear any comments on what we have so far, plus any other > thoughts for pathway-oriented reports/searches that people would like > to have so we can keep the tool evolving in the right direction.> > Best,> > Simon.> > --> > Simon N. Twigger, Ph.D.> Assistant Professor, Department of Physiology> Medical College of Wisconsin> 8701 Watertown Plank Road,> Milwaukee, WI, USA> tel: 414-456-8802> fax: 414-456-6595> AIM/iChat: simontatmcw> > > > > ------------------------------> > Message: 3> Date: Tue, 14 Aug 2007 15:27:00 -0500> From: "De Pons, Jeff" > Subject: [rat-forum] RGD Survey Question Of The Week> To: > Message-ID:> <1448A38A42714048B9C53E473E13CCF0011F961C@davis.hmgc.mcw.edu>> Content-Type: text/plain; charset="us-ascii"> > Skipped content of type multipart/alternative-------------- next part --------------> A non-text attachment was scrubbed...> Name: not available> Type: image/jpeg> Size: 7922 bytes> Desc: image002.jpg> Url : http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070814/24c37b9d/attachment-0001.jpe> > ------------------------------> > Message: 4> Date: Wed, 22 Aug 2007 00:49:06 -0700> From: AKHS > Subject: [rat-forum] Information request> To: Rat Community Forum > Message-ID: <242273.56868.qm@web30408.mail.mud.yahoo.com>> Content-Type: text/plain; charset="iso-8859-1"> > Dear Members of the RCF> > Can you kindly mail me about the weekly cost involved> at your facility to maintain a rat or mice. (kindly> exclude the salary coponent of the workers involved in> it).> > Looking forward to hearing from you.> > Regards> Arun> > > > ____________________________________________________________________________________> Sick sense of humor? Visit Yahoo! TV's > Comedy with an Edge to see what's on, when. > http://tv.yahoo.com/collections/222> > > ------------------------------> > _______________________________________________> rat-forum mailing list> rat-forum@mcw.edu> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> > > End of rat-forum Digest, Vol 5, Issue 1> *************************************** _________________________________________________________________ Messenger Caf? ? open for fun 24/7. Hot games, cool activities served daily. Visit now. http://cafemessenger.com?ocid=TXT_TAGLM_AugWLtagline -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070822/022b547f/attachment-0001.html From paulas at pobox.upenn.edu Thu Aug 23 06:56:14 2007 From: paulas at pobox.upenn.edu (Paula Clifford) Date: Thu Aug 23 11:07:02 2007 Subject: [rat-forum] Information request In-Reply-To: <8F78639AC56F4143B267FE5F5A1B92C8CE2F05@guyton.phys.mcw.edu> References: <242273.56868.qm@web30408.mail.mud.yahoo.com> <8F78639AC56F4143B267FE5F5A1B92C8CE2F05@guyton.phys.mcw.edu> Message-ID: <46CD75DE.7070602@pobox.upenn.edu> At UPenn - our per diem costs are: large mouse cage per day $1.33, small mouse cage per day $.72, rat cage per day $1.13 Kaldunski, Mary wrote: > Per diem alone is currently $2.66 a week per rat, here. > It is going to be increased next year, though I haven't seen what the > increase will be. > > Mary > > Mary L. Kaldunski > Program Coordinator > Dept of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Rd. > Milwaukee, WI 53226 > 414-456-8840 > fax 414-456-6546 > mlkal@mcw.edu > > -----Original Message----- > From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On > Behalf Of AKHS > Sent: Wednesday, August 22, 2007 2:49 AM > To: Rat Community Forum > Subject: [rat-forum] Information request > > Dear Members of the RCF > > Can you kindly mail me about the weekly cost involved > at your facility to maintain a rat or mice. (kindly > exclude the salary coponent of the workers involved in > it). > > Looking forward to hearing from you. > > Regards > Arun > > > > ________________________________________________________________________ > ____________ > Sick sense of humor? Visit Yahoo! TV's > Comedy with an Edge to see what's on, when. > http://tv.yahoo.com/collections/222 > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > >