Hi Matt, I remember that a long time ago I wondered where to download your tfloc program...
Didn't you describe tfloc in this paper? http://www.ncbi.nlm.nih.gov/pubmed/19329064 At the time, I could not find the source code in UCSC's source repository. There seems to be a parser for it in the Galaxy code, but I couldn't find tfloc itself in there either. Is tfloc available somewhere else on the internet? thanks Max <http://www.ncbi.nlm.nih.gov/pubmed/19329064> -- Maximilian Haussler Office:+44 161 27 55980 Mob: +44 7574 246 789 http://www.manchester.ac.uk/research/maximilian.haussler/ On Thu, Mar 10, 2011 at 2:26 PM, Matt Weirauch <weira...@soe.ucsc.edu>wrote: > Hi Pardis, > > Sorry for my delay in response! I'm glad you find the track useful. > The method itself has never been published, so I think the best way to > go would be to cite one of the genome browser papers, and maybe add in > transfac too if you have room. Anyone else can feel free to chime in > here though! > > Matt > > > On Thu, Mar 10, 2011 at 8:41 AM, Pardis Sabeti > <par...@broadinstitute.org> wrote: > > Dear Vanessa, > > > > It was not immediately obvious to me from the TFBS track credits section > > what, if anything, I should cite. It says that the data was generated by > a > > Biobase program and created by Matt Weirauch and Brian Raney, but does > not > > point to anything. I then looked up other papers that used the track, > and > > none of the ones I looked at cite anything. They simply say in the text > that > > they looked at the TFBS track in the UCSC browser (e.g. eFelice, PLoS > One; > > Choy, BMC Genomics) and in one case ref the UCSC url (Cai, Cancer > Research). > > > > I just wanted to be sure that understanding is clear. Perhaps I could do > > what they did i the main text cite the Kent 2002 Gen Res paper. But if > there > > is any better way to do this, I would love your guidance in order to give > > the right attribution. > > > > Pardis > > > > On Tue, Mar 8, 2011 at 4:08 PM, Vanessa Kirkup Swing < > vane...@soe.ucsc.edu> > > wrote: > >> > >> Dear Pardis, > >> > >> Please see our guidelines for citing Genome Browser annotation tracks > >> here: > >> http://genome.cse.ucsc.edu/cite.html > >> > >> To find references specific to a particular Genome Browser track, click > >> on the blue track name on the main Genome Browser display page for the > >> TFBS conserved track in the hg18 assembly. > >> > >> Feel free to contact the mailing list if you have further questions. > >> > >> Vanessa Kirkup Swing > >> UCSC Genome Bioinformatics Group > >> > >> > >> ----- Original Message ----- > >> From: "Pardis Sabeti" <par...@broadinstitute.org> > >> To: genome@soe.ucsc.edu > >> Cc: "Shari Grossman" <shari.r.gross...@gmail.com> > >> Sent: Monday, March 7, 2011 8:09:12 PM > >> Subject: [Genome] How do I reference TFBS conserved track in UCSC? > >> > >> Dear UCSC, > >> > >> We are using the TFBS conserved track in UCSC HG18 created by Matt > >> Weirauch. > >> How would we reference this in a manuscript, > >> > >> Thank you, > >> Pardis > >> _______________________________________________ > >> Genome maillist - Genome@soe.ucsc.edu > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > > > > > -- > > Pardis Sabeti, MD, DPhil > > Assistant Professor, Harvard University > > Center for Systems Biology > > Department of Organismic and Evolutionary Biology > > Broad Institute of MIT and Harvard > > > > phone: (617) 384-5335 > > website: www.sabetilab.org > > > > > > _______________________________________________ > Genome maillist - Genome@soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
