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Question: Is anyone developing an extensible Galaxy-like interface for Bioconductor?
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gravatar for Jarno Tuimala
8.7 years ago by
Jarno Tuimala140
Jarno Tuimala140 wrote:
Hello! We have developed, and continue to develop Chipster, a graphical user interphase build on top of R and Bioconductor. It is currently steered mostly towards DNA microarray data analysis, but it can be easily extended with any R function, Java code or command line tool. Chipster is a client-server system, and it requires a *NIX backend for server components, but the client is platform independent. It is also possible to set up a stand-alone version of Chipster on a Linux machine. As such, it might be a little heavy-weight for your purpose. Currently we have made binaries available in SourceForge, but we are planning on releasing the sources also, since the system is open source. Please see http://chipster.csc.fi/ for more information. If you'd like to get a test license, you can contact us on chipster at csc.fi. Jarno > Date: Fri, 01 Aug 2008 15:52:22 -0400 > From: "Deanne Taylor" <dtaylor at="" hsph.harvard.edu=""> > Subject: [BioC] Is anyone developing an extensible Galaxy-like > interface for Bioconductor? > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <48933135.2DE5.00B2.0 at hsph.harvard.edu> > Content-Type: text/plain; charset=US-ASCII > > Dear all: > > Iis anyone aware of any projects creating an extensible platform that can > act as an interface to Bioconductor that could be used to deliver Bioconductor > methods to non-command-line-using users? > > To save some replies: > > * I am aware of limmaGUI and affylmGUI, but the tcl/tk interface is > frustrating to some users who have difficulty installing tcl/tk independently > while having R recognize it. Macs and some *nix have been particularly > problematic for some reasons. > > * I am also aware of CARMAweb, bioconductor packages and a few other basic > R-web-interfaces, but I would like something more extensible outside of the R > framework that could work both in R and in Python/Perl for example. Something > more modular. > > * I'm thinking something like Galaxy or Bioclipse. I realize Ross Lazarus is > working on Rgenetics against Galaxy and Galaxy might be a good solution. > > If anyone is aware of other projects (beginning or ongoing or planned) in > this area, I'd deeply appreciate getting pointers to them! > > Deanne > > > -- > > --- > Deanne Taylor PhD > Department of Biostatistics > Harvard School of Public Health > 655 Huntington Avenue > Boston, MA 02115 > Office: 617.432.2899 > Fax: 617.432.5619 > dtaylor at hsph.harvard.edu ---------------------------------------------------------------------- ------- Jarno Tuimala, PhD, bioinformatics, CSC, P.O.Box 405, FI-02101 Espoo, Finland tel.: +358 9 457 2226, fax: +358 9 457 2302, e-mail: jarno.tuimala at csc.fi CSC is the Finnish IT Center for Science, http://www.csc.fi/molbio
ADD COMMENTlink modified 8.7 years ago by Ross Lazarus90 • written 8.7 years ago by Jarno Tuimala140
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gravatar for Ross Lazarus
8.7 years ago by
Ross Lazarus90
Ross Lazarus90 wrote:
Mark, just to set the record straight; your statement about lack of persistence for Galaxy histories applies *only* to anonymous (non- logged in) users. Galaxy histories are unlimited in number, and are *permanent* (at least until the main site runs out of disk space) for logged in users. Accounts are free for the taking. Please register an account for yourself one and try it - create and name a couple of histories, run some tools in each one, logout and return. It's one of the many framework features that Galaxy pioneered years ago and I'm sure the Galaxy developers are sincerely flattered to see it imitated in other frameworks :) > Message: 12 > Date: Tue, 5 Aug 2008 09:20:53 +1000 > From: Mark Cowley <m.cowley at="" garvan.org.au=""> > Subject: Re: [BioC] Is anyone developing an extensible Galaxy-like > interface for Bioconductor? > To: Mark Cowley <m.cowley at="" garvan.org.au=""> > Cc: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca="">, > bioconductor at stat.math.ethz.ch > Message-ID: <7B7C47D3-CDD0-420E-9658-CB4929D4FE72 at garvan.org.au> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi list, > Another GUI interface worth mentioning is genePattern, from the folks > at the Broad. It already talks to R (thought not the very latest > version, and thus not the latest BioC), and for every command that you > run, it shows you the actual R (or Matlab) code that is being run. > There are a large number of user submitted modules, suggesting that it > is relatively easy to extend GP for your own purposes. > In this respect, it is similar to galaxy in that you need to design a > simple web page to specify the data and parameters, which then gets > passed to your R code. > Unlike galaxy, the data in GP remains more persistent, so after you > import it, and create and expressionSet style of object, then you can > perform different tasks on that data. The information transmitted in this electronic communica...{{dropped:16}}
ADD COMMENTlink written 8.7 years ago by Ross Lazarus90
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gravatar for Ross Lazarus
8.7 years ago by
Ross Lazarus90
Ross Lazarus90 wrote:
Thanks - for the record, the Trac instance for Galaxy source code and the wiki including mirror setup documentation is at http://g2.trac.bx.psu.edu/ The main analysis (free) site is http://main.g2.bx.psu.edu/ I recommend that you make yourself an account (top right of the page) and login - otherwise your history/histories will not be saved for your next visit. If you create an account and login, all your work in Galaxy will be permanently persisted - at least until we get 48TB of user data - which should take at least another year or two :) Rather than clog up this list, there's a wiki discussing a planned BioC package based expression toolkit for Galaxy at http://esphealth.org/trac/rgalaxy/wiki/BioCGalaxy - anyone wanting to know more or to contribute is welcome to email me privately. I've added FlexArray to the page on potential frameworks at > Message: 3 > Date: Mon, 4 Aug 2008 13:14:43 -0400 > From: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> > Subject: Re: [BioC] Is anyone developing an extensible Galaxy-like > interface for Bioconductor? > To: bioconductor at stat.math.ethz.ch > Message-ID: <1441941682.20080804131443 at mail.mcgill.ca> > Content-Type: text/plain; charset=iso-8859-15 > > Hello, > > Can someone provide a link to Galaxy? > > And since people are providing links, here's one from me: > http://genomequebec.mcgill.ca/FlexArray/ > FlexArray is a microarray statistical data analysis software, > interactive and quite easy to work with, based on Bioconductor, > for Windows. -- Ross Lazarus MBBS MPH, Director of Bioinformatics Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA. The information transmitted in this electronic communica...{{dropped:16}}
ADD COMMENTlink written 8.7 years ago by Ross Lazarus90
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