From bizzaro at bc.edu Tue May 4 14:48:01 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:31 2006 Subject: [Pipet Devel] [Fwd: Sketch and Loci] Message-ID: <372F40E1.23C8D695@bc.edu> This is a reply from the author of Sketch, a Python drawing program. I wrote to him about possibly using his code in Loci. -------------- next part -------------- An embedded message was scrubbed... From: Bernhard Herzog Subject: Re: Sketch and Loci Date: Tue, 4 May 1999 20:16:26 +0200 (MEST) Size: 3295 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990504/0da4ec30/attachment.mht From bizzaro at bc.edu Tue May 4 21:30:42 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:31 2006 Subject: [Pipet Devel] more examples Message-ID: <372F9F42.CC285A99@bc.edu> DNATools for MICROS~1: http://www.crc.dk/phys/A01B04_dnatools.htm Cheerio. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Wed May 5 15:29:44 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:31 2006 Subject: [Pipet Devel] Re: [pyphy] Mavric Tk version References: Message-ID: <37309C27.9DE2D931@bc.edu> (from pyphy; CC to pipet-devel) Rick Ree wrote: > > Jeff: > > How should we refer to Loci/pyphy/mavric when using loci generated tree > > pictures in papers ? Thomas, I'm not sure what you mean by "refer". Are you talking about a reference for a printed journal article? Loci probably won't be generating its own pictures for a while, which leads to Rick's question below. > A related question: is 'pyphy' the same as 'inst-phy' (listed as one of > the components of Loci on the web page)? If so, then maybe we should drop > the name 'mavric' and consolidate it all under one name. For Loci, an "inst" is an "instrument", which is essentially a plug-in to the Loci system and not a stand-alone program. > Also, could someone clarify for me the relationship between the Loci > system and its components -- i.e., are the components just stand-alone > apps that use Loci code, and can communicate with other Loci components? No, components, mostly what we've been calling "loci" or "locuses", are plug-ins. Although it should be possible to make a stand-alone that interfaces with Loci, we will be focusing on accommodating plug-ins. I have been putting together a "tour" of the system. It has no text right now, but a plug-in would start out as a non-GUI "Instrument" and make direct use of (even customize) the "Instrument Panel" and "Slide", which are the GUI components: http://bioinformatics.org/loci/tour/index.html > I'm a little confused. Can I write an application using pyphy code and > call it 'mavric'? (It's silly, and shamelessly self-promoting, but I kind > of like the name :) If by application you mean plug-in, yes. But pyphy and mavric would have to be modified quite a bit. You see, Loci is designed to give a GUI to command-line programs, so you would have to take the non-GUI parts of pyphy/mavric, and make an "instrument". You would then have to specify the GUI: the "instrument panel" for user input and the output that goes to the "slide". As I mentioned above, you could turn pyphy/mavric into a stand-alone that interfaces with Loci, and that may be less work. I don't have any problems with a stand-alone "pyphy/mavric" (I'm still confused about that name :-) that is separate from Loci (not every TOL project has to run under Loci), but I do intend to have an "inst-phy" (phylogenetic instrument) that is a plug-in as part of the Loci core (very basic distribution). Gutten whatever. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Wed May 5 15:55:26 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:31 2006 Subject: [Pipet Devel] check out gnome-control Message-ID: <3730A22E.DA73E806@bc.edu> Locians, Attached is a screenshot of my desktop with the gnome-control-center running. This program and gnome-linuxconf use a system that I think Loci can imitate. If you had the opportunity to set GNOME up on your system, go check them out. On the right side of the window there is a panel that can take on various GUI's, which can be changed on the fly. I have a tour of the Loci model (no text): http://bioinformatics.org/loci/tour/index.html If we use the control-center/linuxconf model, "Slides" can be in the left panel while "Instrument Panels" can be on the right. The "Benchtop" can be on the left while format conversion utilities (not pictured) can be on the right. The "Stage" can be on the left panel while it drawing tools (not pictured) can be on the right. So altogether we'll have 3 types of windows, but the neat part is they can all be the program/applet; we just need an OpenGL canvas on the left and a widget panel on the right. Whaddaya think? Cheers, Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- -------------- next part -------------- A non-text attachment was scrubbed... Name: gnome-control.jpg Type: image/jpeg Size: 25044 bytes Desc: not available Url : http://bioinformatics.org/pipermail/pipet-devel/attachments/19990505/b71f2e0f/gnome-control.jpg From bizzaro at bc.edu Wed May 5 16:10:51 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:31 2006 Subject: [Pipet Devel] plasmid drawing Message-ID: <3730A5CB.1E96A404@bc.edu> Here is a nice example of a plasmid drawing program: http://www.angelfire.com/ne/acaclone/ pDRAW runs on MICROS~1. The Loci way of doing this would be to have a generic plasmid shape in an OpenGL "materials library". This could then be called upon by any instrument/plug-in. Annotation points would be all around the plasmid shape, and they can be marked on the fly. This is all high-level stuff. If a plasmid (or phylogenetic tree, etc.) is to be drawn by a hundred different plug-ins, why have it generated from scratch? Cheers, Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Wed May 5 16:15:45 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: [Pipet Devel] XML for GUI References: <371437CD.13EE7A12@bc.edu> <99041407370000.26490@mrnlinux.hg.med.umich.edu> Message-ID: <3730A6F1.A3FD81F2@bc.edu> "Matthew R. Nelson" wrote: > > On Wed, 14 Apr 1999, J.W. Bizzaro wrote: > > >Another use of XML (yes, another one), would be to describe vector graphics > >(drawn by GILT?). Does anyone know of an existing XML to describe vector > >graphics? > > Yes. Killustrator, the vector drawing program for KDE and the KOffice > application suite, uses XML as its native file format, as do many of the > KOffice components, including KWord, the word processor. The home page > can be found at > > http://koffice.kde.org/ > http://wwwiti.cs.uni-magdeburg.de/~sattler/killustrator.html > Does anyone know of an XML description of OpenGL graphics? I asked on the OpenGL newsgroup but got no response yet. So, how many DTD's will we have now? :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Wed May 5 18:59:53 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] loci_gui module Message-ID: <3730CD69.D6CDA5F2@bc.edu> Locians, The first piece of Loci code is on the CVS server! I made a module called "loci_gui", which contains a simple (very simple; no kill signal handler yet) GTK program with a layout similar to that of gnome-control-center. There is a Linux/x86 executable in there too. If you have GLADE (a very nice RAD-IDE), you can load the interface with the loci_gui.xml file. I plan to replace "drawingarea" with gtkglarea, which is an OpenGL canvas for GTK. If you are new to CVS, here are some instructions: 0. You will need an account on theopenlab 1. If you don't have CVS, go get it. 2. Set the environment variable. For bash, use $ export CVSROOT=':pserver:yourname@bioinformatics.org:/home/cvs' For csh, use $ setenv CVSROOT ':pserver:yourname@bioinformatics.org:/home/cvs' 3. Login. $ cvs login 4. Checkout the module. $ cvs checkout loci_gui This will create a directory called ./loci_gui with everything in it. If you want a tarball, e-mail me. Enjoy. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Thu May 6 01:05:20 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] loci-gui python version Message-ID: <37312310.ADA5079C@bc.edu> Ahem. After playing around with C-GTK code for a while today, I have once again found that Python-GTK is umpteen times easier. So, I made a Python version of loci-gui, sort of. It is in the CVS module "loci-gui". Notice that the C version is loci_gui. Run the Python program loci-gui.py: $ ./loci-gui.py loci-gui.glade The .glade files in the directory are GUI-XML files generated by GLADE. Since I made the C version in glade, I put the .glade file in the directory. What has to be done next though is to hard code the double-paned window in PyGTK and change the GUI-XML mechanism to draw all widgets in the right pane. The left pane will contain a high-level C-GTK widget for the OpenGL molecule and etc. rendering, which will be wrapped in Python. Thanks to James Henstridge for much of the code to get us started here. Bye. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From Thomas.Sicheritz at molbio.uu.se Thu May 6 03:01:42 1999 From: Thomas.Sicheritz at molbio.uu.se (Thomas.Sicheritz@molbio.uu.se) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: [pyphy] Mavric Tk version In-Reply-To: <37309C27.9DE2D931@bc.edu> References: <37309C27.9DE2D931@bc.edu> Message-ID: <14129.15550.577927.594765@beagle.bmc.uu.se> > > > Jeff: > > > How should we refer to Loci/pyphy/mavric when using loci generated tree > > > pictures in papers ? > > Thomas, I'm not sure what you mean by "refer". Are you talking about a > reference for a printed journal article? Loci probably won't be generating its > own pictures for a while, which leads to Rick's question below. The pyphy part of the loci project now includes mavric (both the Gtk and the Tkinter version) - which right now generates trees ready for submitting to a printed journal. I am going to use the module to generate trees for my current paper. - How shall we mention loci/pyphy/mavric ? -thomas -- Sicheritz Ponten Thomas E. Department of Molecular Biology blippblopp@linux.nu BMC, Uppsala University BMC: +46 18 4714214 BOX 590 S-751 24 UPPSALA Sweden Fax +46 18 557723 http://evolution.bmc.uu.se/~thomas Molecular Tcl: http://evolution.bmc.uu.se/~thomas/tcl Molecular Linux: http://evolution.bmc.uu.se/~thomas/mol_linux De Chelonian Mobile ... The Turtle Moves ... From bizzaro at bc.edu Thu May 6 02:16:38 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: [pyphy] Mavric Tk version References: <37309C27.9DE2D931@bc.edu> <14129.15550.577927.594765@beagle.bmc.uu.se> Message-ID: <373133C6.141A700@bc.edu> Thomas.Sicheritz@molbio.uu.se wrote: > > The pyphy part of the loci project now includes mavric (both the Gtk and > the Tkinter version) - which right now generates trees ready for submitting > to a printed journal. I am going to use the module to generate trees for > my current paper. - How shall we mention loci/pyphy/mavric ? If you want a quick reference, you can give the URL to The Open Lab: http://bioinformatics.org/ If you want a short abstract for Loci, a few sentences, I can come up with something. Let me know if this is what you want. As far as pyphy/mavric is concerned, you and Rick would give the best description. Bye. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From Thomas.Sicheritz at molbio.uu.se Thu May 6 03:22:47 1999 From: Thomas.Sicheritz at molbio.uu.se (Thomas.Sicheritz@molbio.uu.se) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: [pyphy] Mavric Tk version In-Reply-To: <373133C6.141A700@bc.edu> References: <37309C27.9DE2D931@bc.edu> <14129.15550.577927.594765@beagle.bmc.uu.se> <373133C6.141A700@bc.edu> Message-ID: <14129.16769.19083.515599@beagle.bmc.uu.se> J.W. Bizzaro writes: > Thomas.Sicheritz@molbio.uu.se wrote: > > > > The pyphy part of the loci project now includes mavric (both the Gtk and > > the Tkinter version) - which right now generates trees ready for submitting > > to a printed journal. I am going to use the module to generate trees for > > my current paper. - How shall we mention loci/pyphy/mavric ? > > If you want a quick reference, you can give the URL to The Open Lab: > > http://bioinformatics.org/ > > If you want a short abstract for Loci, a few sentences, I can come up with > something. Let me know if this is what you want. As far as pyphy/mavric is > concerned, you and Rick would give the best description. Hmm - what do you think ? Something like: :Phylogentic trees were calcaulated with goblin(Sicheritz) blahblahblah and :visualized using Mavric (part of the Loci Project :http://bioinformatics.org/) Auf Wienerschnitzel -thomas -- Sicheritz Ponten Thomas E. Department of Molecular Biology blippblopp@linux.nu BMC, Uppsala University BMC: +46 18 4714214 BOX 590 S-751 24 UPPSALA Sweden Fax +46 18 557723 http://evolution.bmc.uu.se/~thomas Molecular Tcl: http://evolution.bmc.uu.se/~thomas/tcl Molecular Linux: http://evolution.bmc.uu.se/~thomas/mol_linux De Chelonian Mobile ... The Turtle Moves ... From bizzaro at bc.edu Thu May 6 02:51:58 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: [pyphy] Mavric Tk version References: <37309C27.9DE2D931@bc.edu> <14129.15550.577927.594765@beagle.bmc.uu.se> <373133C6.141A700@bc.edu> <14129.16769.19083.515599@beagle.bmc.uu.se> Message-ID: <37313C0E.E2674DDC@bc.edu> Thomas.Sicheritz@molbio.uu.se wrote: > > Hmm - what do you think ? > Something like: > :Phylogentic trees were calcaulated with goblin(Sicheritz) blahblahblah and > :visualized using Mavric (part of the Loci Project > :http://bioinformatics.org/) Hmmm. I guess eventually mavric will be part of Loci, if that's what you intend. I was under the impression that pyphy/mavric was just a Python module. This is particularly true when we consider that we have only made a sketch of how something like pyphy/mavric can be integrated. Is pyphy/mavric meant to work only with Loci? If so, then you can say it is part of The Loci Project. If pyphy/mavric will be separate for some time or only some derivative will be integrated into Loci, you can say it is part of The Open Lab. Loci: http://bioinformatics.org/loci/ > > Auf Wienerschnitzel > -thomas Until hotdog to you too :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From dwrice at indiana.edu Thu May 6 09:28:38 1999 From: dwrice at indiana.edu (Danny Rice) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] loci_gui module In-Reply-To: <3730CD69.D6CDA5F2@bc.edu> References: <3730CD69.D6CDA5F2@bc.edu> Message-ID: <14129.38645.174022.193112@siren.bio.indiana.edu> >If you are new to CVS, here are some instructions: > > 0. You will need an account on theopenlab Where do I get an account? I tried my mailing list password and that didn't work. Danny Rice From rree at oeb.harvard.edu Thu May 6 10:52:16 1999 From: rree at oeb.harvard.edu (Rick Ree) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: [pyphy] Mavric Tk version In-Reply-To: <37313C0E.E2674DDC@bc.edu> Message-ID: J.W. Bizzaro wrote: > Hmmm. I guess eventually mavric will be part of Loci, if that's what you > intend. I was under the impression that pyphy/mavric was just a Python module. > This is particularly true when we consider that we have only made a sketch of > how something like pyphy/mavric can be integrated. Is pyphy/mavric meant to > work only with Loci? If so, then you can say it is part of The Loci Project. > If pyphy/mavric will be separate for some time or only some derivative will be > integrated into Loci, you can say it is part of The Open Lab. I propose that we just refer to the pyphy/mavric package as 'pyphy', with the intention that eventually it could be used in developing the phylogenetic components of Loci. Thomas, you could then just refer to it as "trees were visualized using pyphy, a phylogenetic software toolkit available from The Open Lab (url:)..." or something like that. The name mavric could be used for a stand-alone application, like the tree editor I prototyped in gnome-python and which Thomas converted to Tk. How does that sound? --Rick From bizzaro at bc.edu Thu May 6 11:06:12 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] [Fwd: pDRAW and Loci] Message-ID: <3731AFE4.C2DF4AF7@bc.edu> This is a reply from Kjeld, who I wrote to about his pDRAW program. I mentioned pDRAW on the list yesterday. I'll CC our conversations until he gets on the mailing list. -------------- next part -------------- An embedded message was scrubbed... From: "Kjeld Olesen" Subject: Re: pDRAW and Loci Date: Thu, 06 May 1999 10:26:37 GMT Size: 3172 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990506/f387f032/attachment.mht From bizzaro at bc.edu Thu May 6 11:37:34 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: pDRAW and Loci References: <19990506102637.58771.qmail@hotmail.com> Message-ID: <3731B73E.8916E36B@bc.edu> Kjeld Olesen wrote: > > First of all I should say that, yes, I am interested > in contributing to your Loci suite. Great! > Secondly, I should inform you that pDRAW is programmed > using Visual Basic. Although I have been using both > Turbo Pascal and Delphi at some points, and I can make > basic Javascript programs etc etc, you would > probalby consider me an inexperienced programmer. > At least I do not have any experience of C and only > limited experience with UNIX/Linux. > This could change of course That's okay. I started out with true BASIC back around 1981, and then I learn Pascal in college, which turned out to be somewhat useless (just after I learned it, everyone started switching to C). I did a bit of programming in Delphi recently, which made some use of my Pascal skills. I am still rather new to C, and now I'm learning Python, which will also be used in Loci. So, welcome to the club :-) > Thirdly, I'd like to know some more details of what would be > required of the plasmid drawing plug-in for Loci? > Will this plug-in also have to do the analysis of the > sequence, or will the analysis data be feed from Loci? The model is being refined as we go along, but a "plug-in" is split up into several parts. The first thing I thought you might want to do is make a high-level widget for drawing plasmids, like what you have done for pDRAW. Analysis routines are separate from all GUI's, which is a key feature of Loci. They will be wrapped in a set of Python modules that connect the analytical tool to the rest of Loci. These modules will be cutomized to translate user_input -> analy_tool_input and then analy_tool_output -> output_to_user. Plus they will communicate with a central workspace for monitoring. > Apart from drawing, will the plug-in also have to be able > to print and/or provide some sort of metafile for the clipboard? Ah, yes. Loci also acts as a drawing program for scientific publications, so the drawing widget itself should be able to output some graphics format. I think Postscript may be best. The output from the drawing widget will be transferred to a drawing program. Several drawings can then be combined, and the user can add text and additional graphics. > What will be the anticipated milestones for the Loci project? I'm sorry things are so sketchy right now. It seems that everytime we try to pin down a design, we come up with some more ideas, and of course things change as we see how well or how poorly features can be implemented. I would say that each major component of Loci is a milestone. So, we need (1) a GUI system (which I just started, (2) drawing widgets (one of which I hope you'll help with), (3) the server/app-broker system, (4) wrappers for plug-ins, (5) workspace and drawing tools (also plug-ins I think), and (6) basic plug-ins that can do analyses. This message was sent to the mailing list. You may want to subscribe. Please go to this page: http://bioinformatics.org/mailman/listinfo/pipet-devel/ Kjeld, where are you from? One of the developers is in Sweden. I wondering because your name sounds Scandinavian of course. Let me know about setting up a Linux shell account for you on the system, if you're ready for one. Also, let me know if you need any tips on C and Python, where to get more info. Cheers. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Thu May 6 11:45:23 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] Re: [pyphy] Mavric Tk version References: Message-ID: <3731B913.3324DA45@bc.edu> Rick, That sounds find to me. It seemed to me there were 3 directions to take Pyphy and/or Mavric: (1) A set of Python modules (2) A stand-alone program (3) A Loci plug-in We could and should do all three. So we have (1) Pyphy (Thomas) (2) Mavric (Rick) (3) Loci phylogenetic plug-in(s) (Loci developers) Okay with you, Thomas? Of course you can say Pyphy is developed at The Open Lab (URL). Ciao. Jeff Rick Ree wrote: > > J.W. Bizzaro wrote: > > > Hmmm. I guess eventually mavric will be part of Loci, if that's what you > > intend. I was under the impression that pyphy/mavric was just a Python module. > > This is particularly true when we consider that we have only made a sketch of > > how something like pyphy/mavric can be integrated. Is pyphy/mavric meant to > > work only with Loci? If so, then you can say it is part of The Loci Project. > > If pyphy/mavric will be separate for some time or only some derivative will be > > integrated into Loci, you can say it is part of The Open Lab. > > I propose that we just refer to the pyphy/mavric package as 'pyphy', with > the intention that eventually it could be used in developing the > phylogenetic components of Loci. Thomas, you could then just refer to it > as "trees were visualized using pyphy, a phylogenetic software toolkit > available from The Open Lab (url:)..." or something like that. > > The name mavric could be used for a stand-alone application, like the tree > editor I prototyped in gnome-python and which Thomas converted to Tk. > > How does that sound? > > --Rick > > _______________________________________________ > pipet-devel maillist - pipet-devel@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Thu May 6 16:30:20 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] mockup Message-ID: <3731FBDC.3AA9C57E@bc.edu> Kiddies, Attached is a mockup of what I think the workspace/benchtop should look like. This is once again a slight change from what I've been talking about. I have now put controls and displays together with the workflow diagram. I think Loci should have two windows: The workspace and the figure builder. The workspace I have attached to this e-mail, I believe should contain the workflow diagram (upper left panel), available analysis tools and documents (lower left panel), and controls or displays (right panel). Notice that there are blue squares and red circles drawn on the left. The blue squares are documents and the red circles are analysis tools. The mockup attached shows a mouse cursor over a document (blue square). Every document can be viewed in a display on the right panel. This will require that Loci has a library of viewer tools. As Humberto suggested, these should be binary and downloaded by users choice if not already part of the Loci distribution. Now what is the next choice in the workpath? What can you do with a document? Change it somehow. So we can click on a red circle in the lower left panel, that represents an available analysis tool. The workpath should in fact always alternate between document and analysis tool (blue square and red circles). Of course blue squares and red circles are just for this mockup. The actual program will have various shapes with a small amount of text describing what it is. The red circle we clicked on now appears at the end of the workflow diagram, where the questionmark is in the mockup. But just like every document has a display, every analysis tool has a control panel. And this control panel, specified by the analysis tool (as a part of making the analysis tool a plug-in to Loci) now replaces the display in the right panel. The controls on the right (I'll make a mockup for what this looks like) are mainly field entry boxes for setting the parameters for the analysis tool. A button on the bottom says "OK" or "Proceed", and when clicked, the analysis tool (either local or remote) is sent the commands with the document (previous in the workpath). The analysis tool returns a document, and we start all over again. At any point the user can click back on a shape in the workpath and is presented with the appropriate display or controls on the right. PLUS, the available analysis tool in the lower left panel will change accordingly, and this is where a FORK in the workpath can be create. The user simply chooses a different set of parameters (if an analysis tool was clicked on) or a new analysis tool to send the document to (if a document was clicked on). This is not to mention choreographed analyses, collaboratories, or figure building. Pretty neat, huh? :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- -------------- next part -------------- A non-text attachment was scrubbed... Name: loci-mockup-display-small.jpg Type: image/jpeg Size: 10158 bytes Desc: not available Url : http://bioinformatics.org/pipermail/pipet-devel/attachments/19990506/f98ebbd3/loci-mockup-display-small.jpg From bizzaro at bc.edu Thu May 6 17:00:09 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] nomenclature Message-ID: <373202D9.95466878@bc.edu> Guys, Don't worry about la nomenclature du jour. I'm always changing names. Just as long you get the gist of the project model, that's all that matters. Take the names with a grain of salt. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Thu May 6 23:27:58 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] loci-workspace Message-ID: <37325DBE.CA6902A1@bc.edu> Ahoy. "loci-workspace" is a new module in the CVS. It is a very simple pygnome application I made/modified that is a bit like the mockup I sent earlier, without any graphics. I think you'll be surprised at how simple the source code is. Check it out. Run it under Python: $ python loci-workspace.py What was in loci-gui will be incorporated into loci-workspace. Cheerio. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Fri May 7 18:30:59 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] request for advise Message-ID: <373369A3.9C9CD6D@bc.edu> Locians, I've been thinking about the 3-pane system I have set up for Loci, and I can't see how to resolve one problem. It would be nice if all we had to worry about was 2D graphics, because this is how I would like a plugin to operate: plug-in (analytical tool) called by Loci | | | \| plug-in returns XML describing GUI for input controls | | | \| Loci sets up input controls in right pane (pane 3) | | | \| User puts in parameters, sends parameters to plug-in | | | \| Plug-in does analysis, and returns XML with new data and display information for the right pane Now this is the tricky part. The "display information" can be many different things. As I said, if everything would output 2D display info, we could just use the GNOME canvas, which is already set up in the right pane. But what about 3D displays? Let's suppose OpenGL is all we need for 3D. Then we would have to put an OpenGL canvas in the right pane. That's not so easy, because the window is made with Python. I would need (1) Python bindings to OpenGL, (2) OpenGL bindings to GTK, and (3) Python bindigs to 2. Well, 1 (PyOpenGL) and 2 (GtkGLArea) exist but 3 doesn't. An alternative would be to make the display a separate window and maybe a separate process (like we were originally planning). This way the display could be in PyGNOME or almost anything else, as long as it can work with the PAOS server. So the plug-in would return not only XML but some information about the program to be launched as a display. It sounds nice, but I think this would make Loci considerably more complex. And I am hoping for a nearly 100% Python (except for the analysis tool) implementation, which would not be the case. Can anyone help make (3) the Python bindings to GtkGLArea? I asked the author and the PyGTK maillist, and got no real bites. This may be the best solution. Can we make the GNOME canvas take output from a modeler like DND, and display it as a 2D drawing? Can we have an OpenGL engine without a GUI, process the image and send it as 2D to the GNOME canvas? Any suggestions? Cheerios. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Sat May 8 15:26:37 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] amuzing Message-ID: <37348FED.2CB473F8@bc.edu> http://washingtonpost.com/wp-srv/style/music/features/loci1007.htm From bizzaro at bc.edu Tue May 11 01:34:53 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] [Fwd: Loci] Message-ID: <3737C17D.ADD7168B@bc.edu> >From Alan Williams: -------------- next part -------------- An embedded message was scrubbed... From: Alan Williams Subject: Loci Date: Mon, 10 May 1999 18:44:05 +0000 Size: 3911 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990511/86c48bc0/attachment.mht From bizzaro at bc.edu Tue May 11 01:35:33 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] [Fwd: Loci] Message-ID: <3737C1A5.DC4485F4@bc.edu> Alan replies to my reply: -------------- next part -------------- An embedded message was scrubbed... From: "Alan J. Williams" Subject: Re: Loci Date: Mon, 10 May 1999 14:15:42 -0700 (PDT) Size: 6395 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990511/779bda6e/attachment.mht From bizzaro at bc.edu Tue May 11 02:18:26 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:32 2006 Subject: [Pipet Devel] [Fwd: Loci] References: <3737C1A5.DC4485F4@bc.edu> Message-ID: <3737CBB2.F44822D7@bc.edu> > > I just took a look at it, and it looks good. Thomas Sicheritz from Sweeden (one > > of the early volunteers) was going to make an editor in Python-GTK but has now > > switch to a phylogenetics project, PyPhy, which you probably saw mentioned on > > the list. > I'd be open to providing this functionality. Would it be a core component > or a plug-in? Plug-in I would assume. I'd like to carry the plug-in model to an extreme. In fact, it is hard to identify one program that represents Loci and performs the bulk of the work. This is not so with most applications that use plug-ins. > > We probably won't be able to avoid C altogether, so your experience will be > > helpful. Have you looked into Python? Most people who have, including myself, > > have been amazed at just how nice it is to work with. > I know of it, but have no experience with it. A question for those of you > who have experience, how portable is it from one UNIX system to another? With the exception of the GTK bindings, Python is as portable as Perl. It may be more portable than Tcl/Tk, but I'm not the best judge of that language. Of course I'm talking about the non-GUI Python scripts. And to my knowledge, Python exists on nearly every UNIX variant. > In general, I have had much greater success in recompiling C source code > than source from other languages. (Of course this may be due to my > greater familiarity with C or that the C code my be written better?) I have found compiling C, even between Linux variants, to be unpredictable with about 1 in 4 apps compiling on the first attempt. And C is better at this than C++. With Python, you can make changes to the code at runtime :-) And of course no compiling. > What is the status of developing a LocusML? In reexamining my own work, I > think a well defined DTD would greatly aid in the development of widgets. > IE for the multiseq ed it would be great if the widget itself understood > xml info for the sequence as well as the various markup. Is the plan to > modify BioML or start from scratch? We have had some lengthy discussions about LocusML. The people interested in its development and most qualified to do so are Justin, Humberto, Tim, and Rahul. I may be forgetting someone. We will actually be defining several DTD's, which may be derived from other XML's: Sequence definition: BioML + BSML Structure def: mmCIF/XML + some CML Phylogeny def: ??? probably make our own Database query def: maybe from BLAST/XML Workflow def: make our own GUI def: from GLADE/XML Graphics def: maybe from some KDE programs As far as graphics are concerned, the idea is to define vector (and OpenGL?) graphics so that custom made schematics can be generated by the plug-in, and the plug-in developer can choose some high-level representations...sort of like graphical widgets. > It would seem to me that a quality set of bioinformatic widgets written in > C would be a tremendous resource to several bioinformatics projects going > on. With python wrappers, loci plugins could use them, with perl > wrappers, bioperl users could use them, etc ... Yes. Agreed. And they would be considerable faster in C. Maximum reuse for the components of Loci is an important consideration. It would be nice if the widgets could be compiled into unrelated applications. > > We are using PAOS, which holds some advantages for us. But we are considering a > > CORBA interface that connects the whole of Loci to any CORBA client. > What is PAOS? How is it simmilar/different from CORBA? Check out the local home page for PAOS: http://bioinformatics.org/paos/ How it compares to CORBA is not an easy thing for me to answer, since I have not worked with either for very long. But I do have some thoughts about the advantages of PAOS, which I will put in the next e-mail. > Yeah, I saw the post. I think it is a great idea. I would think this > might be another reason for writting the widgets in C. This would allow > use of the glade lib modified to accept xml info for the bioinformatic > widgets. The trick is connecting the GTK signals to handlers in the plug-in itself. And yes to add bioinformatics widgets to the collection. You may be the best man for that job too. I think it is important to develop an SDK concurrently with Loci. > I also have some experience using PHP and mysql for developing web > interfaces. Of course, once commandline tools are in place, this shouldn't > be too difficult. I have used phplib for doing session management. That's good. Rahul volunteered to help with the Web interface. We may create a separate CVS module and maillist in a little while. > At this point, working on my own machine for development would be easier. > If/When my widgets/programs become useful I would certainly consider > distribution through TOL. Does your web server allow for php scripts? Sure. It's a PentiumI running RedHat Linux 5.2. > Sounds like I should jump right in. How can I get CVS access (The only > cvs experience I have is downloading the current wine code from CVS.) I can create an account for you. There are a few important CVS commands, which I can send to you with your account info. Cheerios. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Tue May 11 02:36:21 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] PAOS vs. CORBA Message-ID: <3737CFE5.54B3A0D0@bc.edu> In response to Alan's question and maybe to answer some yet unasked, here is the reasoning behind the choice of PAOS over CORBA: (1) CORBA bindings are not available for Python under GNU GPL or LGPL. The CORBA system is in fact so different from Python and C (it is closer to C++ and Java) that bindings have been difficult to make (a la the ORBit project). (2) CORBA is a general-purpose object server that we cannot change. PAOS, on the other hand can be changed (we hope :-) to suit our needs, making a special purpose biocomputing system. Having a "Loci system" will allow for a much cleaner integration of tools. (3) Being special purpose and 100% Python, PAOS will be significantly easier than CORBA for new contributors to pick up. Konrad once noted that if the barrier to contributing to Loci is learning CORBA, it may be enough to discourage most contributions. (4) Loci will make use of XML for document exchange and inter-locus communication to such an extent that we will want an object broker that is also an XML parser/writer (if we can build this into PAOS, which goes along with #2). And this is not to mention recent news that CORBA is losing its language independence and being slated to use Java as some kind of intermediate. Cheers. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From hinsen at cnrs-orleans.fr Tue May 11 04:58:03 1999 From: hinsen at cnrs-orleans.fr (Konrad Hinsen) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] request for advise In-Reply-To: <199905081600.MAA01694@bioinformatics.org> (pipet-devel-admin@bioinformatics.org) References: <199905081600.MAA01694@bioinformatics.org> Message-ID: <199905110858.KAA15055@chinon.cnrs-orleans.fr> > But what about 3D displays? Let's suppose OpenGL is all we need for 3D. Then > we would have to put an OpenGL canvas in the right pane. That's not so easy, > because the window is made with Python. I would need (1) Python bindings to > OpenGL, (2) OpenGL bindings to GTK, and (3) Python bindigs to 2. Well, 1 > (PyOpenGL) and 2 (GtkGLArea) exist but 3 doesn't. Then (3) should be created, it will benefit other projects as well! The same combination exists for Tk (using Togl), so it would be nice to have it for GTK as well. > Can we make the GNOME canvas take output from a modeler like DND, > and display it as a 2D drawing? Can we have an OpenGL engine without > a GUI, process the image and send it as 2D to the GNOME canvas? All of this is possible, but slow. Which is significant, because 3D models are of little use unless they can be manipulated, so frequent redrawing must be taken into account. Direct OpenGL output within GTK is clearly the better solution - provided somebody can do it! -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From bizzaro at bc.edu Wed May 12 19:13:45 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] nice python ide Message-ID: <373A0B29.2B4F4FB6@bc.edu> FYI: If you're looking for a decent editor and IDE for Python (and other languages), which also happens to be in GTK (a big plus for me), check out Tide: http://hare.net.au/~neilh/ScintillaTide.html You will want to make sure TideGTK.properties is copied to $HOME/TideGlobal.properties It's a little slow at scrolling, but it has standard Mac/Win keybindings, syntax styling, line numbering in the margin, and starts the Python interpreter from the menu. Cheers. Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Wed May 12 23:27:46 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] cvsweb is up! Message-ID: <373A46B2.F9B9E010@bc.edu> Hey little campers, The CVSWeb server is operational. Check it out: http://bioinformatics.org/cgi-bin/cvsweb.cgi/ In case you didn't know, CVSWeb lets you browse the CVS repository from the Web. It makes life a little easier for us. Woo-hoo! Cheers. Jeff From bizzaro at bc.edu Thu May 13 09:24:02 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] loci-widgets Message-ID: <373AD272.46C6DA15@bc.edu> I made some changes to the CVS: I added loci-widgets, which will contain C, Python-wrapped, and Python widgets to be used by the plug-ins. Check it out. I have an example of the gnome canvas in the directory called testcanvas. The trick (for me) is figuring out how to wrap something like that in Python. I removed loci_gui, loci-gui, and "loci". loci-gui will be incorporated into loci-workspace soon. "loci" was just a test of the CVS. Right now it looks like our modules will be loci-workspace loci-widgets loci-plug-ins loci-server loci-xml loci-sdk :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Thu May 13 23:10:54 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] licensing Message-ID: <373B943E.1A9ED24A@bc.edu> Alan Williams and I discussed some licensing issues that may be of interest to others on the list. The next several messages are forwarded e-mails. -------------- next part -------------- An embedded message was scrubbed... From: "Alan J. Williams" Subject: Re: account Date: Thu, 13 May 1999 09:13:48 -0700 (PDT) Size: 3244 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990513/cbd6d8a4/attachment.mht From bizzaro at bc.edu Thu May 13 23:11:28 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] licensing Message-ID: <373B9460.9EF1EEB0@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: "J.W. Bizzaro" Subject: licensing - was account Date: Thu, 13 May 1999 18:51:23 -0400 Size: 4045 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990513/2c74afb7/attachment.mht From bizzaro at bc.edu Thu May 13 23:11:57 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] licensing Message-ID: <373B947D.A7A055C9@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: "J.W. Bizzaro" Subject: Re: licensing - was account Date: Thu, 13 May 1999 19:11:41 -0400 Size: 2263 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990513/df3002d9/attachment.mht From bizzaro at bc.edu Thu May 13 23:12:32 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] licensing Message-ID: <373B94A0.3C3E3AE9@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: "Alan J. Williams" Subject: Re: licensing - was account Date: Thu, 13 May 1999 16:49:26 -0700 (PDT) Size: 5504 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990513/38c201de/attachment.mht From bizzaro at bc.edu Thu May 13 23:12:53 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] licensing Message-ID: <373B94B5.15441EA5@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: "Alan J. Williams" Subject: Re: licensing - was account Date: Thu, 13 May 1999 16:57:14 -0700 (PDT) Size: 2591 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990513/7469ef00/attachment.mht From bizzaro at bc.edu Thu May 13 23:13:41 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] licensing Message-ID: <373B94E5.3302B601@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: "J.W. Bizzaro" Subject: Re: licensing - was account Date: Thu, 13 May 1999 21:06:12 -0400 Size: 5878 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990513/cf5eda53/attachment.mht From bizzaro at bc.edu Thu May 13 23:14:44 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] licensing Message-ID: <373B9524.62B1F885@bc.edu> -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- -------------- next part -------------- An embedded message was scrubbed... From: "Alan J. Williams" Subject: Re: licensing - was account Date: Thu, 13 May 1999 18:42:00 -0700 (PDT) Size: 2390 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990513/c49714ec/attachment.mht From bizzaro at bc.edu Sun May 16 16:05:25 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:33 2006 Subject: [Pipet Devel] loci-core Message-ID: <373F2505.4FD7C1C9@bc.edu> Locians, I think many of the modules can be consolidated. I have put up "loci-core", which was formally loci-workspace. loci-core should also contain the core widgets, so maybe there is no need for loci-widgets either. The basic plug-in mechanism should also go in loci-core, and maybe even the server. I made a bit more progress toward making the Work Flow Diagram. If you checkout loci-core, you'll see that you can move little boxes around on the canvas. I also separated the WFD from the main Python module, and I'm calling the WFD a "widget", so that I can explore the ins and outs of making high-level GUI widgets. The GLADE/XML mechanism is still not included, but I'm working on it. BTW, where did everybody go? Are you guys still cramming for your finals? It's awfully quiet around here. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From hortiz at neurobio.upr.clu.edu Wed May 19 18:04:33 1999 From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] Announce: xml-mol mail list Message-ID: <199905192204.SAA11922@chimbo.neurobio.upr.clu.edu> Thought some of you might like to keep an eye on this. -------------- next part -------------- An embedded message was scrubbed... From: unknown sender Subject: no subject Date: no date Size: 38 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990519/56a660ee/attachment.mht From paxamr at unix.ccc.nottingham.ac.uk Wed May 19 08:01:00 1999 From: paxamr at unix.ccc.nottingham.ac.uk (adam moore) Date: Fri Feb 10 19:18:34 2006 Subject: Bioperl: Announce: xml-mol mail list In-Reply-To: Message-ID: xml-mol mail list: scope and interests xml-mol is a mail-list for the discussion of issues concerning the implementation of XML-based biological and chemical applications and data with particular reference to sequences and structure. Specific fields of interest include (non-exhaustive list): - Parsing legacy data into XML - Document Object Model (DOM) handling of bioData - Developing open frameworks for XML-aware bio applications xml-mol mail list: FAQ (Frequently asked questions) 1. How do I (un)subscribe? To (un)subscribe to the list send an email with the text '(un)subscribe xml-mol' in the body to majordomo@ala.vsms.nottingham.ac.uk 2. Can I read old messages to this list? A full archive of the list is available at: http://ala.vsms.nottingham.ac.uk/biodom/xml-mol/ 3. What biological data should I discuss here? Any of it! The list scope particularily focuses on molecules, but one of the great things about working in an emerging field is the wide variety of uses / applications that become available every day. Please let us know if you have one! 4. What programming language should I use / discuss here? There are no restrictions on discussing language specific issues, but bear in mind that expertise and interest will vary, and there are some lanaguage-specific mail-lists. Currently there are XML applications being written in (at least) perl, java, C, C++ and python. 5 Why is the FAQ so short? Because the list is so new! Additions will be made over time. Please let me know of any changes you would like made FAQ maintainer: Adam Moore Adam Moore Virtual School of Molecular Sciences School of Pharmaceutical Science, University of Nottingham http://www.vsms.nottingham.ac.uk/vsms/ Personal Page:http://www.ccc.nottingham.ac.uk/~paxamr/ =========== Bioperl Project Mailing List Message Footer ======= Project URL: http://bio.perl.org/ For info about how to (un)subscribe, where messages are archived, etc: http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html ==================================================================== ------- =_aaaaaaaaaa0 Content-Type: text/plain; charset="us-ascii" Content-ID: <11916.927151473.3@chimbo.neurobio.upr.clu.edu> -- Humberto Ortiz Zuazaga Bioinformatics Specialist Institute of Neurobiology hortiz@neurobio.upr.clu.edu ------- =_aaaaaaaaaa0-- From bizzaro at bc.edu Thu May 20 11:37:33 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] Announce: xml-mol mail list References: <199905192204.SAA11922@chimbo.neurobio.upr.clu.edu> Message-ID: <37442C3D.758F976@bc.edu> This is very interesting, and may be of some help. I have communicated with Peter Murray Rust in the past, and even took one of his VSMS courses. He is actually one of the early promoters of XML, before it was even standardized, and of course he wrote the Chemical Markup Language (CML). Perhaps I should announce Loci on that list. It's interesting that they mention Python. Peter has been a big Java fan, and it seems they now have some interest in Perl. :-) Jeff Humberto Ortiz Zuazaga wrote: > > Thought some of you might like to keep an eye on this. > > -------------------------------------------------------------------------------- > > Subject: Bioperl: Announce: xml-mol mail list > Date: Wed, 19 May 1999 13:01:00 +0100 (BST) > From: adam moore > To: vsns-bcd-perl@lists.uni-bielefeld.de > > xml-mol mail list: scope and interests > > xml-mol is a mail-list for the discussion of issues concerning the > implementation of XML-based biological and chemical applications > and data with particular reference to sequences and structure. > > Specific fields of interest include (non-exhaustive list): > - Parsing legacy data into XML > - Document Object Model (DOM) handling of bioData > - Developing open frameworks for XML-aware bio applications > > xml-mol mail list: FAQ (Frequently asked questions) > > 1. How do I (un)subscribe? > > To (un)subscribe to the list send an email with the text > '(un)subscribe xml-mol' in the body to > majordomo@ala.vsms.nottingham.ac.uk > > 2. Can I read old messages to this list? > > A full archive of the list is available at: > http://ala.vsms.nottingham.ac.uk/biodom/xml-mol/ > > 3. What biological data should I discuss here? > > Any of it! The list scope particularily focuses on molecules, but > one of the great things about working in an emerging field is the > wide variety of uses / applications that become available every > day. Please let us know if you have one! > > 4. What programming language should I use / discuss here? > > There are no restrictions on discussing language specific issues, > but bear in mind that expertise and interest will vary, and there > are some lanaguage-specific mail-lists. Currently there are XML > applications being written in (at least) perl, java, C, C++ and > python. > > 5 Why is the FAQ so short? > > Because the list is so new! Additions will be made over time. > Please let me know of any changes you would like made > > FAQ maintainer: Adam Moore > > Adam Moore > Virtual School of Molecular Sciences > School of Pharmaceutical Science, University of Nottingham > http://www.vsms.nottingham.ac.uk/vsms/ > Personal Page:http://www.ccc.nottingham.ac.uk/~paxamr/ > > =========== Bioperl Project Mailing List Message Footer ======= > Project URL: http://bio.perl.org/ > For info about how to (un)subscribe, where messages are archived, etc: > http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html > ==================================================================== > > -------------------------------------------------------------------------------- > -- > Humberto Ortiz Zuazaga > Bioinformatics Specialist > Institute of Neurobiology > hortiz@neurobio.upr.clu.edu -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Fri May 21 17:04:13 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] snapshot Message-ID: <3745CA4D.EC866A88@bc.edu> Locians, If you want to check out how the groovy new GUI is coming along, you can get the CVS module or download a tarball from the Web site: http://bioinformatics.org/loci/download/loci-core-19990521.tar.gz You will of course need gnome-libs and gnome-python to run it. Let me know if you run into any problems. This should give you an idea as to how the Work Flow Diagram will look and work. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Fri May 28 03:06:06 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] update Message-ID: <374E405E.68936F4E@bc.edu> Hey kids, I'm continuing to work on the workflow diagram, and there has been some evolution in the design. I have daringly combined the loci with the diagram itself. Originally, we were going to have boxes represent loci and windows on the X desktop. But I figured we could pretty easily stick the loci onto the workflow diagram. Where boxes would have been connected by lines, little windowlets or applets are connected by lines, and they can be dragged and dropped! There is even a hierarchy of loci, with children being attached to parents, and the children all move when the parent is moved. I made testwidget.py, which will draw out some widgets into the windowlet, and this is supposed to represent a plug-in locus. It's on the CVS. But if you really don't care, you can take a glance at the screenshot attached. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- -------------- next part -------------- A non-text attachment was scrubbed... Name: loci-screenshot-19990527.gif Type: image/gif Size: 9420 bytes Desc: not available Url : http://bioinformatics.org/pipermail/pipet-devel/attachments/19990528/3ef0d16d/loci-screenshot-19990527.gif From bizzaro at bc.edu Fri May 28 14:59:32 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] your tol account Message-ID: <374EE794.CB35926C@bc.edu> If you have an account on theopenlab server, please subscribe to theopenlab mailing list. It is not a very active list, but I would like to use it to contact everyone who has a shell account on the system. Go to this page to subscribe: http://bioinformatics.org/mailman/listinfo/theopenlab Also, I implore you to use SSH and SFTP (secure login) for connecting to the server, if your country allows this type of connection. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Fri May 28 15:25:55 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] XML Message-ID: <374EEDC3.E66C8D55@bc.edu> Locians, The following is a reply I got from Guy Hulbert on the xml-mol mailing list. I would strongly suggest the Loci XML X-perts subscribe to this list, since this is a legitimate attempt to come up with some standards for XML and bioinformatics. It would be nice if we could participate and improve Loci's compatibility with future projects. http://ala.vsms.nottingham.ac.uk/biodom/xml-mol/ Jeff -----------------8<------------------- On Fri, 28 May 1999, J.W. Bizzaro wrote: JWB> Anyway, I am coordinating an ambitious GNU project for UNIX-type systems I'll have to check out your website then. JWB> some ideas: JWB> JWB> Sequence definition: BioML + BSML JWB> Structure def: mmCIF/XML + some CML JWB> Phylogeny def: ??? probably make our own JWB> Database query def: maybe from BLAST/XML JWB> Workflow def: make our own JWB> GUI def: from GLADE/XML JWB> Graphics def: maybe from some KDE programs Previously visual genomics had some restrictions on use of BSML. They still regard this as their intellectual property. See: http://www.visualgenomics.com/bsml/index.html for their current ideas. I don't think this is suitable for a "GNU project". I don't like either BioML or BSML. It seems to me that they are much too large --- trying to provide a complete 'bio-html'. With XML namespaces [ see: http://www.xml.com/xml/pub/1999/01/namespaces.html ] one ought to be able to to put together small DTDs for specialized data. Consider DNA sequences. All one needs is which is a string of the characters CTAG. One might allow ignorable whitespace and base-numbers: 1 tcgattcca gca... 51 gcctacaac acg... ... which is understood by many present applications (without the tags). There is also a standard alphabet which allows ambiguous bases to be included, e.g. 'N' stands for any of A,T,C,G etc. It may be desirable to represent these sequences as where X is the alphabet name. However, to manage DNA sequences, one doesn't need much more than this. Now, this is a bit too small but it would be really nice to have a standard Nucleic acid DTD --- or perhaps "Sequence" DTD. It would have , , and perhaps variations for generalized sequence alphabets. If everyone would use this then the problem of data-interchange between databases is much simplified. Suppose bio??? is some mythical organization which coordinates the standard DTDs and everyone agreed to use them then XML namespaces would allow us to represent (for example) Genbank data like this: [I stole a bit of this from Tim Bray's page on namespaces referenced above] My Sequence blah blah blah ... ... 1 tcgattcca gca... 51 gcctacaac acg... ... and with approiate style sheets, Mozilla and Internet Expoit^H^Hrer would be able to display them. I'm keen to work with anyone on getting these small things set up. As an experiment, I'm planning to play with the Genbank data to create the basic facility to create documents like the above. ---- Guy Hulbert, Systems Manager Bioinformatics Supercomputing Centre (416) 813-8876 555 University Avenue email: guy@bioinfo.sickkids.on.ca The Hospital for Sick Children http: www.bioinfo.sickkids.on.ca Toronto, ON, M5G 1X8, CANADA. From bizzaro at bc.edu Fri May 28 15:52:15 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] Re: XML Message-ID: <374EF3EF.E5944FA2@bc.edu> Guy Hulbert wrote: > > Previously visual genomics had some restrictions on use of BSML. They still > regard this as their intellectual property. See: > http://www.visualgenomics.com/bsml/index.html > for their current ideas. I don't think this is suitable for a "GNU project". Agreed. We have no intention of doing a cut-and-paste of any "proprietary XML" like BSML or BioML. We only wish to judge the approaches taken and see if we could do better. Besides, there really is no patent on BSML or BioML, and it would seem odd trying to close-source an XML, especially when they post the DTD's on the Web sites. > I don't like either BioML or BSML. It seems to me that they are much too > large --- trying to provide a complete 'bio-html'. With XML namespaces > [ see: http://www.xml.com/xml/pub/1999/01/namespaces.html ] > one ought to be able to to put together small DTDs for specialized data. I agree with you 100%! Biological information is (1) too large, (2) too complex, (3) changes too frequently, and (4) is incomplete--much is still unknown. This would make for an enormous moving target for any one DTD. PLUS, there is a mistaken notion with BSML and BioML that bioinformatics == sequence information. What about structure??? > and with approiate style sheets, Mozilla and Internet Expoit^H^Hrer > would be able to display them. It seems the Web browser is trying to become a universal GUI. Either we surrender the desktop and OS to Netscape and MICROS~1, and have everything run through one window, or we continue to make applications with a limited set of functions but that are able to do what they do very well. > I'm keen to work with anyone on getting these small things set up. As > an experiment, I'm planning to play with the Genbank data to create the > basic facility to create documents like the above. GenBank translation is probably the first translation project for Loci. We (myself and a few others working on Loci) would love to help. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Fri May 28 16:08:55 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] [Fwd: Comment on Re: The Loci Project] Message-ID: <374EF7D7.8A334ECD@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: Paul Gordon Subject: Re: Comment on Re: The Loci Project Date: Fri, 28 May 1999 16:40:36 -0300 (ADT) Size: 3740 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990528/eea09c4d/attachment.mht From bizzaro at bc.edu Fri May 28 16:09:10 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] Re: Comment on Re: The Loci Project References: Message-ID: <374EF7E6.A8CBB584@bc.edu> Paul Gordon wrote: > > IMHO: > It's a nice concept, but I think it misses a strong point of BIOML and > BSML. Mozilla and IE can display the sequence with your mixed markup, but > what can you actually *do* with the data? Form and display is provided, > but without an extensive standard markup there isn't much activity > related to the sequence (such as visualization and feature hightlighting > for example of annotated sequence) that the browser can provide to the > user. > > A very small DTD would provide little benefit over straight HTML. If you > just want to exchange DNA, RNA or protein between applications, FASTA is a > pretty simple, common format. With Loci, we are toying with the idea of giving every bio-object, as defined via XML, a unique identification number. This way objects can refer to one another without being necessarily nested, one inside the other. This allows for various, small XML's to be used, even XML's that are unrelated. For example, we intend to use XML for graphics. Should we then define one DTD to represent all biodata plus all graphics? We could, but it would be more practical to break it up. How about phylogenetics? It's not completely compatible with say molecule structure information, and the user will likely care about only one or the other. So should phylogenetics and structure always be used together? What about polysaccharide sequence and structure? That's such a new area but every bit as much a part of biology as DNA sequence. Should the completion of a DTD be held off until every aspect of biology is understood? Should there be one big DTD that has to be changed with every new issue of a scientific journal? Of course Loci is not really concerned with Web representations, so I'm not addressing those issues. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Fri May 28 18:57:23 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] [Fwd: Comment on Re: The Loci Project] Message-ID: <374F1F53.54FBEA79@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: Guy Hulbert Subject: Re: Comment on Re: The Loci Project Date: Fri, 28 May 1999 18:23:21 -0400 (EDT) Size: 3441 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990528/663d6b3f/attachment.mht From bizzaro at bc.edu Fri May 28 19:34:18 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:34 2006 Subject: [Pipet Devel] Re: Comment on Re: The Loci Project References: Message-ID: <374F27FA.8C47CB74@bc.edu> Guy Hulbert wrote: > > NO NO NO. You'll be reported to the XML police. XML is for *DATA* the > tag tells you what the data represents. Style sheets are for presentation. Maybe I misled you by not explaining the role of XML for graphics in Loci. It is not simply for specifying presentation or layout. It actually works in parallel with the biodata. In Loci, GRAPHICS ARE DATA. In fact almost everything is data and treated as objects or widgets. So Loci plug-ins pass XML objects to other components. Just as one component would pass biodata XML, another would pass an XML object that contains a schematic to be drawn in vector graphics. The XML's aren't even mixed. Biodata XML contains just biodata and says nothing about layout. Maybe this isn't the W3-ordained way to display XML in a Web browser, because we're not using DOM or XSL. But Loci has some unique uses of XML, and recall that it is not even a Web browser-based program. In a sense, we are using XML more like SGML, but of course XML will be simpler for us. For the biodata anyway, we are interested in using a standardized, non-commercial XML, and even helping develop it. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Mon May 31 22:53:59 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:35 2006 Subject: [Pipet Devel] [Fwd: Comment on Re: The Loci Project] Message-ID: <37534B47.5535A766@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: Guy Hulbert Subject: Re: Comment on Re: The Loci Project Date: Mon, 31 May 1999 07:24:21 -0400 (EDT) Size: 3789 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990601/0eb78c75/attachment.mht