From bizzaro at bc.edu Thu Jul 1 09:40:48 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:41 2006 Subject: [Pipet Devel] workspace shapshot, July 1 Message-ID: <377B6FE0.7D8476E7@bc.edu> Release early and often, as they say. Well, I know that most of the people on this list don't have CVS access, so here is a tarball: http://theopenlab.um.edu/loci/download/loci-core-19990701.tar.gz Note that this is what has been on the CVS for about a week, so if you checked out the module a little while ago (Humberto), there's no need to update. Requirements: gnome-libs >= 1.0.10 gnome-python >= 1.0.3 Of course it doesn't do much of anything yet, but I am happy with the look and feel. Let me know what you think or if you have any ideas. To get an idea as to what my plans are for the workspace, I have pasted a message from June 6, "cunstructing the command line": Locians, As the development continues, it appears the users will be able to construct their own gui's by connecting loci together. This will involve the use of an XML similar to Damon Chaplin's Glade XML, which was really made just to save projects. Here is an example of Glade XML. It's simply a button placed in a container and in a window. -----------------8<------------------ project1 pixmaps C False False gladesrc.c gladesrc.h gladesig.c gladesig.h GtkWindow window1 window1 GTK_WINDOW_TOPLEVEL GTK_WIN_POS_NONE True True False GtkFixed fixed1 GtkButton button1 32 16 112 40 True -----------------8<------------------ Note: James Henstridge already made a Python script to generate a PyGTK gui from Glade XML. You can see that the widgets here are Gtk widgets; of course, this is for Gtk. But let's say we make higher level, composite widgets (the "megawidgets" I've been talking about). Instead simple gui widgets, some of Loci's composite widgets will generate the options of a command-line. (Some composite widgets will be biowidgets of a sort.) For example, in the build phase we start off with a windowlet/locus containing a composite widget that is an option to choose the name of a program. This may simply have a text entry box where the user can type in the name. Next, the user can add a flag option. A new locus appears, and they are presented with a pull down list of all flags, -a to -Z. Underneath that is a text entry box that goes with the flag, because sometimes a flag option expects a term to be added. And the user can actually specify types and ranges for any option. Say the program that the gui is being built for requires an integer after the -n flag. In the build phase, the user can set this using some radio button or something. At this point the user will see several composite widgets, each with its own locus, all connected with lines. Selecting the parent locus (the first one made), the user can pull down a menu and cause them all to be merged into a functional, gui representation of a command-line. Now that the locus is out of the build phase, only the options that were not previously set are visible. I mentioned a couple months ago that there are some programs meant to wrap command-lines in a gui. GGUI is one that uses wizards: http://www.greysite.com/ggui/ I also found TkWorld, which is like GGUI: http://www.tkworld.org/ But Loci is not meant to be just a command-line generator. It will do this, but much more will be included. For one, Loci will keep biodata in a standardized XML format. This will require conversion utilities: one for LocusML -> program-format, and one for program-format -> LocusML. This is because, unlike simple UNIX shell utilities, most bioinfo programs have specific format requirements. Another issue I don't believe is addressed so nicely by GGUI and TkWorld, is piping. Loci's loci will, by the nature of the bioinfo programs used, make extensive use of piping or connecting output to input. And this is supposed to occur seamlessly over the Internet; not something normally done in the UNIX shell. So what will the resultant gui XML look like? I think that when the loci are combined, the XML's can be concatonated. And the user can take them back apart, recombine them as they wish, and even save/store them. A really neat result is that a user can make some unique concoction and then send it across the Internet to someone else using Loci. Rapid locus development and sharing will be important to Loci's success. Well, if you read this far, thank you. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Thu Jul 1 09:44:15 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] the correct address, I think Message-ID: <377B70AF.AE1B23D1@bc.edu> uml.edu, not um.edu :-) http://bioinformatics.org/loci/download/loci-core-19990701.tar.gz Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Sun Jul 4 17:08:02 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] Web pages (was: Gary Van Domselaar joins!) References: <3772F826.4DB9F04B@bc.edu> Message-ID: <377FCD32.CE2F2D6B@bc.edu> Gary Van Domselaar wrote: > > For my first task I think I should probably flesh out the web site a > bit. What would you like to see? I personally like the GNOME web page > design (http://www.gnome.org), which is quite a bit like the loci pages > are now. Gary, by "GNOME web page design", do you mean the layout or the graphics? One of the first Loci (then called TULIP) pages used both the graphics and layout of GNOME. I have sice changed it quite a bit. The current design looks a little more like Freshmeat's. I have also tried to keep the Loci pages looking like other TOL pages. Can you come up with a one-page prototype so we can get an idea as to how it would look? > For starters I propose the following structure: > > Main Page - Logo, blurb, and News. > > User Info > Introduction to Loci > Tour of Loci > Download > Documentation > > Developer Info > Introduction (Joining, Background Info & Development Tools) > Loci Architecture & Systems > CVS instructions (CVS server?) > Mailing List > > This structure is based loosely on the gnome web pages. > Some other things: User Screenshots Developer List of developers Development snapshots We need some CVS instructions for TOL in general. Loci can just have a link to the TOL page for that. > I made a couple Loci logos last week when i was playing with the GIMP > and POVRAY. You can check them out at > http://redpoll.pharmacy.ualberta.ca/~gvd/loci/ > Give me your input and I will GIMP up an 'official' logo when I get back Wow! I think they're really nice. I had an idea of my own. I will sketch it up and post it here soon to see what everyone thinks of it. >From a recent message: > > I hope to have > the web pages a little more complete by then, so that they can visit the site. I might > need your help for technical review. Sure. There are some rather lengthy discussions that we had about Loci's design. I was thinking that they might be turned into technical essays that we can post. > A month isnt a lot of time, so I think I will have > to do the pages quickly rather than correctly. I'm not super-happy with netscape > composer, but I think I will develop the pages with it for now. What have you used before? > I'd like the option of > writing php for dynamic web page generation, but I dont think it is activated in the > apache web server right now. Hmmm. Alan Williams (Alan@TheWilliamsFamily.org) just offered to do some PHP scripting too. Maybe you too can work together on this? One thing we were looking to do was put a table of contents on the right side of each Loci page. But it would have to be dynamically generated in case there are some changes. I started doing this statically, but it just became too much to keep up with as I added new pages. :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From gvd at redpoll.pharmacy.ualberta.ca Sun Jul 4 21:54:50 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] Web pages In-Reply-To: <199907050018.SAA00608@gvd.v-wave.com> Message-ID: On Sun, 4 Jul 1999, Gary Van Domselaar wrote: > Gary, by "GNOME web page design", do you mean the layout or the graphics? Both. > > Can you come up with a one-page prototype so we can get an idea as to how it > would look? no prob. > Some other things: User Screenshots Developer List of developers Development snapshots Got it. I'd like the option of > > writing php for dynamic web page generation, but I dont think it is activated in the > > apache web server right now. > > Hmmm. Alan Williams (Alan@TheWilliamsFamily.org) just offered to do some PHP > scripting too. Maybe you too can work together on this? One thing we were > looking to do was put a table of contents on the right side of each Loci page. > But it would have to be dynamically generated in case there are some changes. I > started doing this statically, but it just became too much to keep up with as I > added new pages. > Let me see what I can do with php. Website Meta Language (WML) (http://www.engelschall.com/sw/wml/) may also be useful here. > From a recent message: > > > > I hope to have > > the web pages a little more complete by then, so that they can visit the site. I might > > need your help for technical review. > > Sure. There are some rather lengthy discussions that we had about Loci's > design. I was thinking that they might be turned into technical essays that we > can post. Thats what I was thinking as well. > > > A month isnt a lot of time, so I think I will have > > to do the pages quickly rather than correctly. I'm not super-happy with netscape > > composer, but I think I will develop the pages with it for now. > > What have you used before? Composer, vi, and perl. The problem with composer is the way it gets confused about nested bullets and list items, and the way it reformats the html. A friend of mine suggested I use cascading style sheets to format the web pages, which is more line with the XML concept than standard html. I'll check out some tutorials on it and then decide if i can tackle the loci pages that way. Would I be correct to assume that the html generation technology that we adopt will be used for TOL pages as well? --Gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From stein at fmppr.fmnh.org Wed Jul 7 17:38:36 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] bioinformatics online info References: Message-ID: <3783C8DC.958469C7@fmnh.org> Just thought I'd share my latest bioinformatics web finds (my Museum curator colleagues really don't care about this stuff): http://www.bioinfo.de/isb/ In their set of inaugural articles, take a peek at SEView, a java applet for viewing molecular sequence data. http://www.bitsjournal.com/bits.html Some interesting reading (more likely for the powers-that-be) on the merging of IT and biology (and voila, we have bioinformatics). A useful (albeit somewhat biased) article out of Oracle on CORBA and its applications to bioinformatics projects. -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 -------------------------- From bizzaro at bc.edu Wed Jul 7 23:49:43 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] bioinformatics online info References: <3783C8DC.958469C7@fmnh.org> Message-ID: <37841FD7.1411C2D9@bc.edu> Eeek. New journals are popping up everywhere! So how many are there now? Bioinformatics (CABIOS) Journal of Computational Biology Gene COMBIS ISB BITS Any others? How about BioInfo :-) Jeff "J. Steinbachs" wrote: > > Just thought I'd share my latest bioinformatics web finds (my Museum > curator colleagues really don't care about this stuff): > > http://www.bioinfo.de/isb/ > In their set of inaugural articles, take a peek at SEView, a java applet > for viewing molecular sequence data. > > http://www.bitsjournal.com/bits.html > Some interesting reading (more likely for the powers-that-be) on the > merging of IT and biology (and voila, we have bioinformatics). A useful > (albeit somewhat biased) article out of Oracle on CORBA and its > applications to bioinformatics projects. > > -------------------------- > Jennifer Steinbachs > Computational Biologist > Dept. of Botany > The Field Museum > Chicago, IL 60605-2496 > > office: 312-665-7810 > fax: 312-665-7158 > -------------------------- > > _______________________________________________ > 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 Wed Jul 7 23:56:21 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] bioinformatics online info References: <3783C8DC.958469C7@fmnh.org> Message-ID: <37842165.C2C38A00@bc.edu> "J. Steinbachs" wrote: > > http://www.bioinfo.de/isb/ > In their set of inaugural articles, take a peek at SEView, a java applet > for viewing molecular sequence data. Wow! Hey this is exactly what we're looking for some of the translators to do! This is required reading :-) Here is a direct link: http://www.bioinfo.de/isb/1998/01/0003/ Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From pmr at sanger.ac.uk Thu Jul 8 04:06:39 1999 From: pmr at sanger.ac.uk (Peter Rice) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] bioinformatics online info In-Reply-To: <37841FD7.1411C2D9@bc.edu> (bizzaro@bc.edu) References: <3783C8DC.958469C7@fmnh.org> <37841FD7.1411C2D9@bc.edu> Message-ID: <199907080806.JAA12870@europa.sanger.ac.uk> Jeff Bizarro writes: >Eeek. New journals are popping up everywhere! So how many are there now? EMBnet.News http://www.uk.embnet.org/embnet.news/ BioInformer (from EBI) http://bioinformer.ebi.ac.uk/ BioInform http://www.bioinform.com/ UK CCP11 Newsletter http://www.hgmp.mrc.ac.uk/CCP11/newsletter/ Genome Research also publishes genome bioinformatics articles -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From David.Lapointe at umassmed.edu Thu Jul 8 11:00:07 1999 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] bioinformatics online info Message-ID: <93307F07DE63D211B2F30000F808E9E501644D05@edunivexch02.umassmed.edu> How about Genome Research Protein Science [?] David Lapointe Manager - Research Computing Services UMass Medical School Worcester, MA 01655 508/856-5141 > -----Original Message----- > From: J.W. Bizzaro [mailto:bizzaro@bc.edu] > Sent: Wednesday, July 07, 1999 11:50 PM > To: pipet-devel@bioinformatics.org > Subject: Re: [Pipet Devel] bioinformatics online info > > > Eeek. New journals are popping up everywhere! So how many > are there now? > > Bioinformatics (CABIOS) > Journal of Computational Biology > Gene COMBIS > ISB > BITS > > Any others? How about > > BioInfo > > :-) > Jeff > > > "J. Steinbachs" wrote: > > > > Just thought I'd share my latest bioinformatics web finds (my Museum > > curator colleagues really don't care about this stuff): > > > > http://www.bioinfo.de/isb/ > > In their set of inaugural articles, take a peek at SEView, > a java applet > > for viewing molecular sequence data. > > > > http://www.bitsjournal.com/bits.html > > Some interesting reading (more likely for the powers-that-be) on the > > merging of IT and biology (and voila, we have > bioinformatics). A useful > > (albeit somewhat biased) article out of Oracle on CORBA and its > > applications to bioinformatics projects. > > > > -------------------------- > > Jennifer Steinbachs > > Computational Biologist > > Dept. of Botany > > The Field Museum > > Chicago, IL 60605-2496 > > > > office: 312-665-7810 > > fax: 312-665-7158 > > -------------------------- > > > > _______________________________________________ > > 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/ > -- > > _______________________________________________ > pipet-devel maillist - pipet-devel@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel > From stein at fmppr.fmnh.org Thu Jul 8 11:19:44 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] bioinformatics online info References: <3783C8DC.958469C7@fmnh.org> <37841FD7.1411C2D9@bc.edu> Message-ID: <3784C190.3C78994D@fmnh.org> "J.W. Bizzaro" wrote: > > Eeek. New journals are popping up everywhere! So how many are there now? > > Bioinformatics (CABIOS) > Journal of Computational Biology > Gene COMBIS Sadly, if you go to Elsevier's site and read the little scrolly banner in the bottom (in Netscape), you will notice that Gene-COMBIS has been discontinued as of this year. I'm putting together a set of bookmarks for online computational biology related journals. When I get them together (and get a machine set up), I'll point you to the URL. -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 -------------------------- From bizzaro at bc.edu Fri Jul 9 01:48:35 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] freshmeat announcement Message-ID: <37858D33.4AFB0D3B@bc.edu> I just made the first announcement about Loci at freshmeat.net. I know we don't have much to show, but I intended this to be a general announcement about the project. In the future, we can just post "loci-core X.X.X", "loci-daemon X.X.X", etc. In just over an hour, the page got hit as much as it does in a whole day :-) Here is what I posted: The Loci Project (alpha) J.W. Bizzaro - July 08th 1999, 23:05 EST Loci is a network-distributed system of clients and servers ("loci") for computational biology research. The loci are data, high-level widgets, analysis programs (command-line), data translators, vector drawing programs, and any combination of these. They are represented as nodes on a graphical "work flow diagram" (WFD) and can be connected in a manner akin to Unix piping. In a sense, Loci is a graphical scripting language where users can build, customize and execute their own scriptlets via the WFD. Plus, connecting loci across the Internet, can form world-wide collaboratives and an infinitely extensible set of loci. Numerous development tools used include Python, GTK+ and the GNOME environment: CORBA, DOM, XML and so on. Although Loci is being developed for computational biology (for which it is highly suited), the system's core is not dependent on a particular data type. THIS IS ALPHA SOFTWARE! Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From bizzaro at bc.edu Fri Jul 9 16:31:17 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal] Message-ID: <37865C15.F2CF764F@bc.edu> Locians, Ferdinando Villa posted this message to one of the Gnome mailing lists. His idea reminded me so much of Loci that I contacted him. I will forward the rest of our correspondence next. Jeff -------------- next part -------------- An embedded message was scrubbed... From: Ferdinando Villa Subject: Meta-Application Interface: a proposal Date: Thu, 17 Jun 1999 14:42:39 -0400 (EDT) Size: 7004 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/55724ed1/attachment.mht From bizzaro at bc.edu Fri Jul 9 16:32:25 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal] Message-ID: <37865C59.F99A9594@bc.edu> I guess I did send this message to the list before. But here it is again. -------------- next part -------------- An embedded message was scrubbed... From: "J.W. Bizzaro" Subject: Re: Meta-Application Interface: a proposal Date: Fri, 18 Jun 1999 00:19:07 +0000 Size: 8791 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/5dd02d9a/attachment.mht From bizzaro at bc.edu Fri Jul 9 16:32:51 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:42 2006 Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal] Message-ID: <37865C73.2E131A88@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: Ferdinando Villa Subject: Re: Meta-Application Interface: a proposal Date: Fri, 9 Jul 1999 10:12:02 -0400 (EDT) Size: 6196 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/2bfb8509/attachment.mht From bizzaro at bc.edu Fri Jul 9 16:33:37 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal] Message-ID: <37865CA1.F91D955@bc.edu> -------------- next part -------------- An embedded message was scrubbed... From: "J.W. Bizzaro" Subject: Re: Meta-Application Interface: a proposal Date: Fri, 09 Jul 1999 19:48:10 +0000 Size: 6813 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/85d94a02/attachment.mht From bizzaro at bc.edu Fri Jul 9 16:34:47 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal] Message-ID: <37865CE7.10662C54@bc.edu> I hope to continue this conversation on this list. -------------- next part -------------- An embedded message was scrubbed... From: Ferdinando Villa Subject: Re: Meta-Application Interface: a proposal Date: Fri, 9 Jul 1999 16:08:26 -0400 (EDT) Size: 5214 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/fa082f4f/attachment.mht From bizzaro at bc.edu Fri Jul 9 18:35:32 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] loci-core-19990708 Message-ID: <37867934.DEA4E9B0@bc.edu> Here is a new snapshot: http://bioinformatics.org/loci/download/loci-core-19990708.tar.gz For those new to the list, remember that all you can do is move some pretty little boxes around. This is NOT a functional application yet. You need: gnome-libs 1.0.10 gnome-python 1.0.3 And of course what those need. I got scrollbars for the workspace now. The next thing I'll be working on is getting the workspace/canvas to grow in size when an object pushes beyond the boundaries. Any ideas? I think if I can get the bounds of all objects, I can check them against the bounds when they are moved (or maybe just dropped) and then resize the workspace if needed. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From justin at ukans.edu Fri Jul 9 23:37:24 1999 From: justin at ukans.edu (Justin Bradford) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] DOM/gdome update Message-ID: I've contacted the author of gdome, and am actively tracking its development. Unfortunately, little is being done with it currently. Most of its development is being driven by gill (an SVG application). Anyway, I've talked to the primary author of gdome. His plans for the sliding DOM have been set aside, and they are currently concentrated on implementing a straight DOM interface over CORBA. He was very interested in my ideas on a simple wire protocol (something that would not require CORBA, necessarily), and I'll be getting back to him with a proposal for an intelligent client-side gdome interface (which resolves many of the problems with DOM over CORBA). However, the first priority for this side of development is probably python bindings to CORBA. I'll be checking into that this weekend. With the new design, supposedly new language bindings are not too difficult. Hopefully, I can get something working soon which will allow use of GNOME's CORBA stuff. We can use the convential gdome system for the interim, and eventually, the new, more efficient (but not quite traditional DOM) interface will be available for implementing our various tools. Is everyone ok with the idea of a centralized gdome system holding the Loci data? Plugins (viewers, editors, etc) all deal with the data via the gdome interface. It offers some very cool benefits with little (Loci unique) code, so as event notification, locking, etc. I've been busy at Genentech lately, but I just wrapped up a project, so I can hopefully do something for Loci now, besides write emails about what I'm going to do ;) And for anyone who cares, Genentech (the original biotech company, based in San Francisco) is a very cool place. And it looks like they're going to give me a job next January, and probably pay for grad school. The bioinformatics/biocomputing departments are expanding rapidly for anyone looking for jobs :) Justin From bizzaro at bc.edu Sat Jul 10 01:17:13 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] DOM/gdome update References: Message-ID: <3786D759.2B5260FC@bc.edu> Justin Bradford wrote: > > I've contacted the author of gdome, and am actively tracking its > development. Unfortunately, little is being done with it currently. Most > of its development is being driven by gill (an SVG application). Hi Justin. Who's the author of gdome? > Anyway, I've talked to the primary author of gdome. His plans for the > sliding DOM have been set aside, and they are currently concentrated on > implementing a straight DOM interface over CORBA. He was very interested > in my ideas on a simple wire protocol (something that would not require > CORBA, necessarily), and I'll be getting back to him with a proposal for > an intelligent client-side gdome interface (which resolves many of the > problems with DOM over CORBA). Hmmm. I don't recall if you mentioned a "wire protocol" before on this list. Feel free to share the proposal with us when it's ready. > However, the first priority for this side of development is probably > python bindings to CORBA. I'll be checking into that this weekend. With > the new design, supposedly new language bindings are not too difficult. Great. Did you post on the ORBit list that you'll be working on the bindings? The Python newsgroup might be a good place to announce that too. > Hopefully, I can get something working soon which will allow use of > GNOME's CORBA stuff. We can use the convential gdome system for the > interim, and eventually, the new, more efficient (but not quite > traditional DOM) interface will be available for implementing our various > tools. Neeto. But I think most of us will need a primer on using CORBA and DOM. Is there some documentation that you think would be helpful? > Is everyone ok with the idea of a centralized gdome system holding the > Loci data? Plugins (viewers, editors, etc) all deal with the data via the > gdome interface. It offers some very cool benefits with little (Loci > unique) code, so as event notification, locking, etc. The last messages I posted from Ferdinando pointed out that there are quite a few guys around with somewhat similar plans for Gnome. If we all work together, we will have something that much better and sooner. And I think if we decide to use Gnome, we should get more than just our feet wet and try to work on some Gnome development (blur the line between Gnome and Loci). This way we will understand the system better and get to know (and maybe get some help from) the Gnome developers. Some of those guys (and some of you guys :-) are way ahead of me, and I'd love to work with them. > I've been busy at Genentech lately, but I just wrapped up a project, so I > can hopefully do something for Loci now, besides write emails about what > I'm going to do ;) :-) > And for anyone who cares, Genentech (the original biotech company, based > in San Francisco) is a very cool place. And it looks like they're going to > give me a job next January, and probably pay for grad school. The > bioinformatics/biocomputing departments are expanding rapidly for anyone > looking for jobs :) Congratulations! Cheers. Jeff P.S. We got 301 hits on the Loci page Friday, due mostly to the Freshmeat post. And there are 2 new subscribers to the list. -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From hortiz at neurobio.upr.clu.edu Mon Jul 12 11:17:59 1999 From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] DOM/gdome update In-Reply-To: Your message of "Fri, 09 Jul 1999 22:37:24 EST." Message-ID: <199907121518.LAA18473@chimbo.neurobio.upr.clu.edu> > Is everyone ok with the idea of a centralized gdome system holding the > Loci data? Plugins (viewers, editors, etc) all deal with the data via the > gdome interface. It offers some very cool benefits with little (Loci > unique) code, so as event notification, locking, etc. This sounds great, especially if you can keep the API the same over corba or the light weight transport. -- Humberto Ortiz Zuazaga Bioinformatics Specialist Institute of Neurobiology hortiz@neurobio.upr.clu.edu From bizzaro at bc.edu Mon Jul 12 21:35:45 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] gnome-filer (fwd) Message-ID: <378A97F1.BD3F6D91@bc.edu> Here is a message from David Orme to Ferdinando Villa about gnome-filer. Recall that Ferdinando said he would send us this message. Jeff -------------- next part -------------- An embedded message was scrubbed... From: Ferdinando Villa Subject: Re: Meta-Application Interface: a proposal (fwd) Date: Mon, 12 Jul 1999 11:42:36 -0400 (EDT) Size: 1245 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990713/1f795057/attachment.mht From bizzaro at bc.edu Mon Jul 12 22:37:59 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:43 2006 Subject: [Pipet Devel] [Fwd: The Loci Project] Message-ID: <378AA687.E6C33B47@bc.edu> Here is a reply from Thomas Junier, co-author of SEView. Recall that Jennifer sent us a link to his article in ISB: http://www.bioinfo.de/isb/1998/01/0003/ I sent a message to Thomas and the other author, Philipp, to see if they would like to help with Loci. Jeff -------------- next part -------------- An embedded message was scrubbed... From: Thomas Junier Subject: Re: The Loci Project Date: Sun, 11 Jul 1999 10:11:32 +0200 Size: 4240 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990713/38c33b1d/attachment.mht From bizzaro at bc.edu Tue Jul 13 00:13:34 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] Web server is down for upgrading Message-ID: <378ABCEE.BCBD6C7B@bc.edu> Greetings. We're sorry to say that Web access to The Open Lab will be unavailable for a short while. We are trying to upgrade some of the software. However, other services like SSH are still up. I will send another message when the Web server is operational. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Tue Jul 13 18:35:51 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] Web server is back up Message-ID: <378BBF47.F5B370B8@bc.edu> Hello again. We ran into some configuration problems. The server is back up and running, but PHP support is still in the queue, so to speek. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Wed Jul 14 10:56:01 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] Another (java) bioinformatics tool Message-ID: <378CA501.BF684F80@fmnh.org> To all: I stumbled across this reference last night. Anybody know anything about it? (free? commercial? good? bad?) Sadly, I don't have access to this journal either in paper format (except through interlibrary loan) or online... Gregg A. Helt, Suzanna Lewis, Ann E. Loraine, and Gerald M. Rubin BioViews: Java-Based Tools for Genomic Data Visualization Genome Res. 1998 8: 291-305. [Abstract] [Full Text] -jennifer -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 -------------------------- From hortiz at neurobio.upr.clu.edu Wed Jul 14 11:33:50 1999 From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] Another (java) bioinformatics tool In-Reply-To: Your message of "Wed, 14 Jul 1999 09:56:01 EST." <378CA501.BF684F80@fmnh.org> Message-ID: <199907141533.LAA01385@chimbo.neurobio.upr.clu.edu> > I stumbled across this reference last night. Anybody know anything > about it? > > Gregg A. Helt, Suzanna Lewis, Ann E. Loraine, and Gerald M. Rubin > BioViews: Java-Based Tools for Genomic Data Visualization > Genome Res. 1998 8: 291-305. [Abstract] [Full Text] Try: http://www.fruitfly.org/bioviews/ I thought this project had been merged with the BioWidgets for Java project, but this web page looks pretty active. You can find some more links off my computational molecular biology page: http://www.neurobio.upr.clu.edu/~hortiz/cmb/ -- Humberto Ortiz Zuazaga Bioinformatics Specialist Institute of Neurobiology hortiz@neurobio.upr.clu.edu From hortiz at neurobio.upr.clu.edu Wed Jul 14 11:37:20 1999 From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] Another (java) bioinformatics tool In-Reply-To: Your message of "Wed, 14 Jul 1999 09:56:01 EST." <378CA501.BF684F80@fmnh.org> Message-ID: <199907141537.LAA01415@chimbo.neurobio.upr.clu.edu> > BioViews: Java-Based Tools for Genomic Data Visualization Sorry, damn frames, the correct url is: http://www.fruitfly.org/displays/ -- Humberto Ortiz Zuazaga Bioinformatics Specialist Institute of Neurobiology hortiz@neurobio.upr.clu.edu From gvd at redpoll.pharmacy.ualberta.ca Thu Jul 15 02:35:14 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] PHP is up In-Reply-To: <378BBF47.F5B370B8@bc.edu> from "J.W. Bizzaro" at Jul 13, 99 10:35:51 pm Message-ID: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca> Locians, PHP is now running on the apache server. Some of you may know that PHP is a server-parsed web-scripting language that allows you to make sophisticated dynamic HTML pages easily. I've also allowed read-only access to user directories for those of you who are interested in doing some php development. I'll use it primarily to index the website, but its useful for other things too. One of PHP's strongest features is database integration (excite uses PHP). I was thinking it might be nice some day to use PHP to create a "bioinformatics portal" as a resource to the community. I'll get to work on some template pages for loci hopefully sometime next week. --Gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From justin at ukans.edu Thu Jul 15 05:29:33 1999 From: justin at ukans.edu (Justin Bradford) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] PHP is up In-Reply-To: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca> Message-ID: > I was thinking it might be nice some day > to use PHP to create a "bioinformatics portal" as a resource to the > community. Ok, but I get in on the IPO, right? ;) Oh, has anyone here seem Spotfire's analysis software? I caught a demo today, and some of the UI stuff was pretty interesting. It was basically just a graphing engine, but it you could really tweak the display and go through a lot of data visually, very quickly. Justin From David.Lapointe at umassmed.edu Thu Jul 15 11:46:34 1999 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] PHP is up Message-ID: <93307F07DE63D211B2F30000F808E9E501644D19@edunivexch02.umassmed.edu> Yes, I saw an article and a review in the HMSBeagle this week. It reminded me of some AVS applications for SciVi that I have seen in the past. Basically dealing with the problem of multidimensional data visualization. The review of Spotfire seemed a little less than glowing. David Lapointe Manager - Research Computing Services UMass Medical School Worcester, MA 01655 508/856-5141 > -----Original Message----- > From: Justin Bradford [mailto:justin@ukans.edu] > Sent: Thursday, July 15, 1999 5:30 AM > To: pipet-devel@bioinformatics.org > Subject: Re: [Pipet Devel] PHP is up > > > > I was thinking it might be nice some day > > to use PHP to create a "bioinformatics portal" as a resource to the > > community. > > Ok, but I get in on the IPO, right? ;) > > Oh, has anyone here seem Spotfire's analysis software? I caught a demo > today, and some of the UI stuff was pretty interesting. It > was basically > just a graphing engine, but it you could really tweak the > display and go > through a lot of data visually, very quickly. > > Justin > > > _______________________________________________ > pipet-devel maillist - pipet-devel@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel > From bizzaro at bc.edu Thu Jul 15 23:14:10 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] PHP is up References: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca> Message-ID: <378EA382.98F11F34@bc.edu> Gary Van Domselaar wrote: > I was thinking it might be nice some day > to use PHP to create a "bioinformatics portal" as a resource to the > community. That may be what BioInfo is in some ways: http://bioinformatics.org/bioinfo/ What do you think should be in a bioinformatics portal? :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Thu Jul 15 23:45:01 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:44 2006 Subject: [Pipet Devel] XML Script Message-ID: <378EAABD.D156864C@bc.edu> Interesting: http://www.xmlscript.org/ I wonder how this would merge with the Workflow Diagram's "graphical command language". Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From stein at fmppr.fmnh.org Fri Jul 16 13:32:52 1999 From: stein at fmppr.fmnh.org (J. Steinbachs) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] UMN's CompBio resources References: <199907141537.LAA01415@chimbo.neurobio.upr.clu.edu> Message-ID: <378F6CC4.14E12147@fmnh.org> More online resources... U. Minnesota's Computational Biology Center: http://www.cbc.umn.edu/ In their "research projects -> papers" links, check out http://www.cbc.umn.edu/VirtLibrary/Shoop/SAC93/SAC93.paper.ss.html -------------------------- Jennifer Steinbachs Computational Biologist Dept. of Botany The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 email: stein@fmnh.org -------------------------- From bizzaro at bc.edu Mon Jul 19 01:20:02 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] gamora Message-ID: <3792B582.85FECAE6@bc.edu> Some similarities to Loci: http://gamora.org/ A little hard to grasp. It's not a bioinformatics app. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Mon Jul 19 01:43:31 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] PHP is up References: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca> <378EA382.98F11F34@bc.edu> Message-ID: <3792BB03.64E45411@redpoll.pharmacy.ualberta.ca> J.W. Bizzaro wrote: > > That may be what BioInfo is in some ways: > > http://bioinformatics.org/bioinfo/ > > What do you think should be in a bioinformatics portal? > TOL's bioinfo is _exactly_ what I was thinking ;-) Add hot current events in bioinformatics with a hierachically organized database like yahoo. Then we pass an XML standard for bioinformatics documents that allows us to catalog them in our database. Once XML takes over the Internet we release a web-crawler that updates the database automagically. Then we sit back and get rich and fat. --Gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada http://redpoll.pharmacy.ualberta.ca/~gvd From bizzaro at bc.edu Mon Jul 19 06:58:51 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] GtkGLArea gets Python wrapper Message-ID: <379304EB.8EAA2327@bc.edu> Locians, Very good news: James Henstridge writes: > In other news, I have added a wrapper for gtkglarea to pygtk. There are a > few examples in the examples/gl directory, including a translation of the > mesa gears demo. To use it, you will also need the PyOpenGL package. GtkGLArea is the Gtk drawing area/widget for OpenGL: http://www.student.oulu.fi/~jlof/gtkglarea/ I wrote to James about making a Python wrapper for it, and well, he just did. The bottom line for us is that we can make Python-based widgets for Loci to render 3D models. Very cool. This brings us another step closer to integrating AMMP and MMTk. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From Alan at TheWilliamsFamily.org Mon Jul 19 10:23:38 1999 From: Alan at TheWilliamsFamily.org (Alan J. Williams) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] PHP is up In-Reply-To: <3792BB03.64E45411@redpoll.pharmacy.ualberta.ca> Message-ID: Along these lines, I have started to put together a bioinformatics and molecular biology jump site at www.molbio.org. Currently the only thing up and running is the news service. It allows for posting to molbio.org by anyone from the web. I want to add a catalog of web resources that can be updated by anyone from the web before I announce the site, which is why I haven't mentioned it to date. On Sun, 18 Jul 1999, Gary Van Domselaar wrote: > > What do you think should be in a bioinformatics portal? > > TOL's bioinfo is _exactly_ what I was thinking ;-) Add hot current > events in bioinformatics with a hierachically organized database like > yahoo. Then we pass an XML standard for bioinformatics documents that > allows us to catalog them in our database. Once XML takes over the > Internet we release a web-crawler that updates the database > automagically. Then we sit back and get rich and fat. ************************************************************************ Alan Williams ------------------------------------------------------------------------ University of California, Riverside "Where observation is concerned, Dept. of Botany and Plant Sciences chance favors the prepared mind." Alan@TheWilliamsFamily.org -- Louis Pasteur ************************************************************************ From finklesk at Op.Net Mon Jul 19 11:48:24 1999 From: finklesk at Op.Net (NNY) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] GtkGLArea gets Python wrapper In-Reply-To: <379304EB.8EAA2327@bc.edu> Message-ID: hi! maybe i missed out on this before... i gather from this that you want everything to be written in python? if whatever you want me to do is to be written in python, where can i find more info on python programming? -greg http://www.op.net/~finklesk/index.html "The problem is not that the world is full of fools. The problem is that lightning isn't being distributed right." - Mark Twain On Mon, 19 Jul 1999, J.W. Bizzaro wrote: > Locians, > > Very good news: > > James Henstridge writes: > > > In other news, I have added a wrapper for gtkglarea to pygtk. There are a > > few examples in the examples/gl directory, including a translation of the > > mesa gears demo. To use it, you will also need the PyOpenGL package. > > GtkGLArea is the Gtk drawing area/widget for OpenGL: > > http://www.student.oulu.fi/~jlof/gtkglarea/ > > I wrote to James about making a Python wrapper for it, and well, he just did. > The bottom line for us is that we can make Python-based widgets for Loci to > render 3D models. Very cool. This brings us another step closer to integrating > AMMP and MMTk. > > > Cheers. > Jeff > -- > +------------------------------------+ > | | > | J.W. Bizzaro | > | jeff@bioinformatics.org | > | | > | THE OPEN COLLABORATORY | > | FOR MOLECULAR BIOINFORMATICS | > | | > | http://bioinformatics.org/ | > | | > +------------------------------------+ > > _______________________________________________ > pipet-devel maillist - pipet-devel@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel > > From bizzaro at bc.edu Tue Jul 20 02:05:01 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] GtkGLArea gets Python wrapper References: Message-ID: <3794118D.554520F8@bc.edu> NNY wrote: > > maybe i missed out on this before... i gather from this that you want > everything to be written in python? Hi Greg. The confusion comes from the fact that Loci's design has been changing so much, as has been the role of Python. At one point I might have said we should strive for 100% Python, and use C only if we really have to. But recently some of us, particularly Justin, Humberto and Alan, have put the CORBA (and other object models) option back on the table. The greatest advantage of using these models is perhaps language-independence. So, Python will not always be REQUIRED for Loci development. Where does Python stand in the big picture now? Well, it will always play a major role doing what it does extremely well: acting as a glue and scripting language for Loci. We plan to make the major GUI components, such as the Workspace, in Python-GTK. BUT, CORBA et al will allow us to make non-Python plug-ins/widgets/loci. Depending on the uniqueness of the widget/locus, use of Python will be more or less a part of making one. For example, if a widget/locus outputs to a GtkGLArea canvas, the widget/locus can call it via CORBA, and it probably won't need any Python wrappers. But if the widget/locus needs a custom drawing area, we'll have to use Python to put it in the Workspace. > if whatever you want me to do is to be > written in python, where can i find more info on python programming? You'll find some links about learning Python-Gtk/Gnome at the PyG Tools page: http://bioinformatics.org/pygtools/ You can also check out the Python page: http://www.python.org/ A REALLY good book, if you want to go that route, is Learning Python Mark Lutz and David Ascher O'Reilly, 1999 ISBN 1-56592-464-9 But what was I hoping you could do for Loci? After all, I asked you to help; you didn't volunteer. We need a molecule modeling widget/locus for starters: a plug-in that can render 3D, OpenGL molecules. Fortunately, we have two complementary projects to base this on. Rob Harrison has much of the C code to display molecules. His program is AMMP (Another Molecular Modeling Program): http://asterix.jci.tju.edu/ammp.html And of course you have your mg^2 modeler and experience with OpenGL. I think we can combine much of what we have into a widget/locus without a lot of new code. Will this require Python? I think we can either use the Python-GtkGLArea wrapper or make it all in C and then write our own wrapper. But if we make a Python-based widget/locus, we'll have more reuse. Cheers. Jeff > > -greg > > http://www.op.net/~finklesk/index.html > > "The problem is not that the world is full of fools. The problem is that > lightning isn't being distributed right." - Mark Twain > > On Mon, 19 Jul 1999, J.W. Bizzaro wrote: > > > Locians, > > > > Very good news: > > > > James Henstridge writes: > > > > > In other news, I have added a wrapper for gtkglarea to pygtk. There are a > > > few examples in the examples/gl directory, including a translation of the > > > mesa gears demo. To use it, you will also need the PyOpenGL package. > > > > GtkGLArea is the Gtk drawing area/widget for OpenGL: > > > > http://www.student.oulu.fi/~jlof/gtkglarea/ > > > > I wrote to James about making a Python wrapper for it, and well, he just did. > > The bottom line for us is that we can make Python-based widgets for Loci to > > render 3D models. Very cool. This brings us another step closer to integrating > > AMMP and MMTk. > > > > > > Cheers. > > Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Tue Jul 20 08:19:35 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] Re: The Loci Project References: <199907110811.KAA14566@pcisrec-d402b.unil.ch> Message-ID: <37946957.AC8FD765@bc.edu> Hello Thomas. I'm sorry that I took so long to get back to you. Thomas Junier wrote: > > All I can say is that I'm very pleased, but I sincerely wonder if I can be of > any help, because I know close to nothing about Python (I'm more of the C/Perl/ > Java world), as to CORBA, DOM and XML I have some idea about what they do, but > not much. Of course, I could start learning all this. :-) Python is being used as a glue language for Loci. Knowledge of it would be helpful but should not be required. We are aiming for a language-neutral system, a la CORBA. So, we're not forcing anyone to pick up a book on Python and start reading ;-) > > I > > think what you have done is an important building block for Loci. > > Well, I'm all the more pleased, but since it's based on Perl and Java, won't it > be hard to integrate it into Loci ? Regarding language, as long as a "translator" can connect to CORBA, the language shouldn't matter. If we use SEView (or a derivative), we will have to work these object models into it. I think we could also use your help with defining a generic "translator" for I/O. The definition should be such that someone can write one in the language of their choosing. We can take a look at SEView and make sort of a generic algorithm that can be used as a blueprint. (That might even be publishable.) > So my answer is that I'm interested, but I'm not sure how I can be useful. If I > first have to learn Python, CORBA, XML and friends, it'll be some time before I > can be productive, I'm afraid. On the other hand, if my Perl/C/Java skills can > be put to use, that would allow me to start working sooner. Well, most of us will need a lesson in CORBA. C works well with Python, and we're sure to have a bit of it in Loci. Actually, most Loci developers are C coders and only a few joined knowing Python, CORBA, etc. We have a few Perl hackers here too, but Python has some obvious strengths for what we need to do. > One thing I could not find on the Loci page: what kind of collaboration do you > have with EMBOSS ? Peter Rice, the coordinator of EMBOSS, reads our list and I read theirs. (He's sure to read this :-) And we've corresponded a few times, but that's about it. If I can take the liberty to speak for them, they are developing a command-line based system much in the spirit of the GCG Wisconsin Package. They have chosen not to choose a GUI because there are several existing that can interface with the EMBOSS command-line (Loci could be on that list but doesn't really "exist"). We would like to make translators (here's where you guys come in) to interface EMBOSS with Loci, but EMBOSS has taken no official position on Loci. BTW, have you spoken to Philipp about Loci? I did not get a message back from him. Does he still work with you? Would you like to join our mailing list? http://bioinformatics.org/mailman/listinfo/pipet-devel/ I can also make an account for you on our server. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Tue Jul 20 08:30:36 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] BioInfo (was: PHP is up) References: Message-ID: <37946BEC.21DCE3DF@bc.edu> "Alan J. Williams" wrote: > > Along these lines, I have started to put together a bioinformatics and > molecular biology jump site at www.molbio.org. Currently the only thing > up and running is the news service. It allows for posting to molbio.org > by anyone from the web. I want to add a catalog of web resources that can > be updated by anyone from the web before I announce the site, which is why > I haven't mentioned it to date. I just took a peek at what you have, and it looks very nice. Are you planning on selling advertising? BioInfo will probably become a portal but more specific to bioinformatics. We are looking to add longer feature articles/editorials, Yahoo!-like links pages (BioWho? or BioHoo!), and I think an events calendar would be nice too. Let me know when you are ready to announce molbio.org and I'll post it on BioInfo. Cheers. Jeff > > On Sun, 18 Jul 1999, Gary Van Domselaar wrote: > > > What do you think should be in a bioinformatics portal? > > > > TOL's bioinfo is _exactly_ what I was thinking ;-) Add hot current > > events in bioinformatics with a hierachically organized database like > > yahoo. Then we pass an XML standard for bioinformatics documents that > > allows us to catalog them in our database. Once XML takes over the > > Internet we release a web-crawler that updates the database > > automagically. Then we sit back and get rich and fat. > -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From pmr at sanger.ac.uk Tue Jul 20 10:44:24 1999 From: pmr at sanger.ac.uk (Peter Rice) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] Re: The Loci Project In-Reply-To: <37946957.AC8FD765@bc.edu> (bizzaro@bc.edu) References: <199907110811.KAA14566@pcisrec-d402b.unil.ch> <37946957.AC8FD765@bc.edu> Message-ID: <199907201444.OAA23090@unst.sanger.ac.uk> Jeff Bizarro wrote: >Thomas Junier wrote: >> One thing I could not find on the Loci page: what kind of >> collaboration do you have with EMBOSS ? >Peter Rice, the coordinator of EMBOSS, reads our list and I read >theirs. (He's sure to read this :-) And we've corresponded a few >times, but that's about it. Yup, I'm here :-) >If I can take the liberty to speak for them, they are developing a >command-line based system much in the spirit of the GCG Wisconsin >Package. They have chosen not to choose a GUI because there are >several existing that can interface with the EMBOSS command-line >(Loci could be on that list but doesn't really "exist"). We would >like to make translators (here's where you guys come in) to interface >EMBOSS with Loci, but EMBOSS has taken no official position on Loci. EMBOSS appears to be command line based, but internally it uses a simple "AJAX command definition" file (the idea comes from VMS). These "ACD" files can be converted to other GUI definitions, so that we hope to automate implementing EMBOSS under most other GUIs in bioinformatics. There are many of these around the EMBnet community and beyond. Examples are BioNavigator (eBioinformatics and EMBnet Australia) AppLab (Martin Senger, EBI), W2H (Martin Senger and EMBnet Germany), www2gcg (EMBnet Belgium), SRS applications (EBI and Lion), ACEDB utilities (Sanger Centre and Montpelier), Staden (Rodger Staden, Cambridge), SeqPup (Don Gilbert, Indiana). No doubt there are others and I would be interested to hear of your favourites. Each has its own definition format, but all have similar content. ACD files define everything that an application needs, and have extensions which EMBOSS ignores to allow HTML forms and other GUIs to be specified. These are very easy to extend. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From finklesk at Op.Net Tue Jul 20 23:44:27 1999 From: finklesk at Op.Net (NNY) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] GtkGLArea gets Python wrapper In-Reply-To: <3794118D.554520F8@bc.edu> Message-ID: sounds fine. i'll look into AMMP. i'm on standby. wake me when you want me to do some coding :) later -greg http://www.op.net/~finklesk/index.html "The problem is not that the world is full of fools. The problem is that lightning isn't being distributed right." - Mark Twain On Tue, 20 Jul 1999, J.W. Bizzaro wrote: > NNY wrote: > > > > maybe i missed out on this before... i gather from this that you want > > everything to be written in python? > > Hi Greg. The confusion comes from the fact that Loci's design has been changing > so much, as has been the role of Python. At one point I might have said we > should strive for 100% Python, and use C only if we really have to. But > recently some of us, particularly Justin, Humberto and Alan, have put the CORBA > (and other object models) option back on the table. The greatest advantage of > using these models is perhaps language-independence. So, Python will not always > be REQUIRED for Loci development. > > Where does Python stand in the big picture now? Well, it will always play a > major role doing what it does extremely well: acting as a glue and scripting > language for Loci. We plan to make the major GUI components, such as the > Workspace, in Python-GTK. BUT, CORBA et al will allow us to make non-Python > plug-ins/widgets/loci. > > Depending on the uniqueness of the widget/locus, use of Python will be more or > less a part of making one. For example, if a widget/locus outputs to a > GtkGLArea canvas, the widget/locus can call it via CORBA, and it probably won't > need any Python wrappers. But if the widget/locus needs a custom drawing area, > we'll have to use Python to put it in the Workspace. > > > if whatever you want me to do is to be > > written in python, where can i find more info on python programming? > > You'll find some links about learning Python-Gtk/Gnome at the PyG Tools page: > > http://bioinformatics.org/pygtools/ > > You can also check out the Python page: > > http://www.python.org/ > > A REALLY good book, if you want to go that route, is > > Learning Python > Mark Lutz and David Ascher > O'Reilly, 1999 > ISBN 1-56592-464-9 > > But what was I hoping you could do for Loci? After all, I asked you to help; > you didn't volunteer. We need a molecule modeling widget/locus for starters: a > plug-in that can render 3D, OpenGL molecules. Fortunately, we have two > complementary projects to base this on. Rob Harrison has much of the C code to > display molecules. His program is AMMP (Another Molecular Modeling Program): > > http://asterix.jci.tju.edu/ammp.html > > And of course you have your mg^2 modeler and experience with OpenGL. I think we > can combine much of what we have into a widget/locus without a lot of new code. > Will this require Python? I think we can either use the Python-GtkGLArea > wrapper or make it all in C and then write our own wrapper. But if we make a > Python-based widget/locus, we'll have more reuse. > > > Cheers. > Jeff > > > > > > -greg > > > > http://www.op.net/~finklesk/index.html > > > > "The problem is not that the world is full of fools. The problem is that > > lightning isn't being distributed right." - Mark Twain > > > > On Mon, 19 Jul 1999, J.W. Bizzaro wrote: > > > > > Locians, > > > > > > Very good news: > > > > > > James Henstridge writes: > > > > > > > In other news, I have added a wrapper for gtkglarea to pygtk. There are a > > > > few examples in the examples/gl directory, including a translation of the > > > > mesa gears demo. To use it, you will also need the PyOpenGL package. > > > > > > GtkGLArea is the Gtk drawing area/widget for OpenGL: > > > > > > http://www.student.oulu.fi/~jlof/gtkglarea/ > > > > > > I wrote to James about making a Python wrapper for it, and well, he just did. > > > The bottom line for us is that we can make Python-based widgets for Loci to > > > render 3D models. Very cool. This brings us another step closer to integrating > > > AMMP and MMTk. > > > > > > > > > Cheers. > > > Jeff > > -- > +------------------------------------+ > | | > | J.W. Bizzaro | > | jeff@bioinformatics.org | > | | > | THE OPEN COLLABORATORY | > | FOR MOLECULAR BIOINFORMATICS | > | | > | http://bioinformatics.org/ | > | | > +------------------------------------+ > > _______________________________________________ > pipet-devel maillist - pipet-devel@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-devel > > From bizzaro at bc.edu Wed Jul 21 10:22:59 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] some info on Gnome Message-ID: <3795D7C3.ECF0A184@bc.edu> Locians, I came across some articles at the "RedHat Knowledge Base" about Gnome. (I think they come from the "whitepapers".) A few of these may be good to read if you want an introduction to some of the Gnome technologies we are planning on using in Loci: Gnome Technologies http://www.redhat.com/knowledgebase/gtg/ Gnome Components http://www.redhat.com/knowledgebase/Components/ CORBA and Gnome http://www.redhat.com/knowledgebase/ORBit/ Gnome Canvas http://www.redhat.com/knowledgebase/canvas/ Cheerios. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Thu Jul 22 06:19:18 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] GTKML Message-ID: <3796F026.5B5B1C4C@bc.edu> Locians, I came across another XML for defining a Gtk GUI. It is not related to GLADE/XML, which I had been planning on using to define locus GUI's, but we're sure to glean some more knowledge from this. Here is a short description and the URL: GTKML stands for "GTK Markup Language". Its purpose is to create an XML document format for defining GTK-based user interfaces. The benefits of such a standard would include that any GTKML-compliant language binding/framework could be used with any GTKML-compliant visual editor, rapid application development, end-users of an application can edit/alter/extend the user-interface without altering code, end-users can easily create language-translations of GTKML documents and share them with others, and more. http://www.k-3d.com/index_gtkml.html :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Sun Jul 25 12:14:29 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] dbXML Message-ID: <379B37E5.FEA5435E@bc.edu> Locians, I found an announcement for the dbXML project at Freshmeat. This appears to be what we were discussing a short while ago: If we're using all XML for our data, why not use an XML-based database? Well, we weren't aware of any at the time. Here's the announcement (Justin, is this guy related to you?): dbXML project now online Tom Bradford - July 22nd 1999, 04:55 EST The dbXML project is a development effort with the ultimate goal of producing a high-performance client/server DBMS for XML-based structured documents. Overall, the theory is that you could speed up database retrieval incredibly if you did not have to join tables constantly to retrieve structured data. So many programs are written to import and export tabular query results to and from XML that it seems like somewhat of a useless step. Why not just store entire structured documents as single entities and retrieve whole or partial documents with simple SQL queries? This is the goal of the dbXML project. The project is only a little more than one week old and is actively looking for talented volunteer contributors. http://www.dbxml.org They are looking for help. Maybe we can kill two birds with one stone here. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From justin at ukans.edu Sun Jul 25 19:14:23 1999 From: justin at ukans.edu (Justin Bradford) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] dbXML In-Reply-To: <379B37E5.FEA5435E@bc.edu> Message-ID: > If we're using all XML for our data, > why not use an XML-based database? Well, we weren't aware of any at > the time. > Here's the announcement (Justin, is this guy related to you?): Yeah. I've been looking at various XML databases, search engines, query languages, etc. I missed this one, however, but I'll take a look at it, as we'll ultimately want something like this. > Tom Bradford - July 22nd 1999, 04:55 EST Hey, this guy has my last name, too. Justin From gvd at redpoll.pharmacy.ualberta.ca Mon Jul 26 03:18:05 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] Web Page Update Message-ID: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca> Locians, As you may know, I have been working on upgrading the web server with PHP. I recently installed the mysql relational database on theopenlab box, so now we can use PHP with mysql (joy!). Jeff pointed out a cst-calendar proggy that uses mysql with php. i installed it on my home box: http://gvd.v-wave.com/~gvd/calendar/index.php3 if you like it i can instal it on the openlab server for the bioinfo portal. I had a little bit of trouble turning on the server-side includes for theopenlab apache server, this resulted in a 'broken' stats page and counter. I personally am not too fond of the web stats generator that was being used (big brother): it logs and displays visitor information like operationg system and stuff-- good stuff for script kiddies. for your consideration i put the webalizer on there instead. Just click the 'view the statistics' link at the bottom of theopenlab main page to check it out. Big brother is still there, but if you want to view it i suggest to password protect it first. I also placed a php/sql counter on theopenlab index and loci index pages. If you like them i will keep them. I think they look fine. Finally, I have begun working on a template for the new web page design. point your browser to http://bioinformatics.org/dev/ and tell me what you think (its still very rough). --Gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada From bizzaro at bc.edu Mon Jul 26 06:30:11 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] Re: Web Page Update References: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca> Message-ID: <379C38B3.222E07B6@bc.edu> Hi Gary! I guess you just answered my question about Webalizer, and I was also wondering what happened to BigBro Stats :-) Gary Van Domselaar wrote: > > As you may know, I have been working on upgrading the web server with > PHP. I recently installed the mysql relational database on theopenlab > box, so now we can use PHP with mysql (joy!). Great. Thank you! > Jeff pointed out a > cst-calendar proggy that uses mysql with php. i installed it on my home > box: > http://gvd.v-wave.com/~gvd/calendar/index.php3 > if you like it i can instal it on the openlab server for the bioinfo portal. I think it lacks a whole-year view. It would be nice if there were clickable "horizontal bars" in such a view showing the duration of a long event like a conference. Do you know what I mean? Do you know of any other calendars? Maybe we can request this feature. > I had a little bit of trouble turning on the server-side includes for > theopenlab apache server, this resulted in a 'broken' stats page and > counter. I personally am not too fond of the web stats generator that > was being used (big brother): it logs and displays visitor information > like operationg system and stuff-- good stuff for script kiddies. for > your consideration i put the webalizer on there instead. Just click the > 'view the statistics' link at the bottom of theopenlab main page to check > it out. Big brother is still there, but if you want to view it i suggest > to password protect it first. Oh. I didn't think it was a security problem, but I guess you know more about that than I do. Webalizer looks nice. As long as I/we can get an idea as to what the activity is on the server. > I also placed a php/sql counter on theopenlab index and loci index > pages. If you like them i will keep them. I think they look fine. They look fine to me too. > Finally, I have begun working on a template for the new web page design. > > point your browser to > http://bioinformatics.org/dev/ > and tell me what you think (its still very rough). I like the title and the background. The background looks like a Bowie Poag image; is it? I don't think the menu area color (robin's egg?) matches the background though. BTW, did you catch the tag that goes in the body? The news program actually generates index.shtml from index.template. goes in index.template. I still need to post my logo idea too. Anyone else have an idea for a logo? Nice work, Gary. Thank you. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From David.Lapointe at umassmed.edu Mon Jul 26 10:22:07 1999 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] dbXML Message-ID: <93307F07DE63D211B2F30000F808E9E501644D47@edunivexch02.umassmed.edu> Along these lines, this may be of interest. http://www.w3.org/XML/RDB.html David Lapointe Manager - Research Computing Services UMass Medical School Worcester, MA 01655 508/856-5141 > -----Original Message----- > From: J.W. Bizzaro [mailto:bizzaro@bc.edu] > Sent: Sunday, July 25, 1999 12:14 PM > To: pipet-devel > Subject: [Pipet Devel] dbXML > > > Locians, > > I found an announcement for the dbXML project at Freshmeat. > This appears to be > what we were discussing a short while ago: If we're using all > XML for our data, > why not use an XML-based database? Well, we weren't aware of > any at the time. > Here's the announcement (Justin, is this guy related to you?): > > dbXML project now online > Tom Bradford - July 22nd 1999, 04:55 EST > > The dbXML project is a development effort with the ultimate goal of > producing a high-performance client/server DBMS for XML-based > structured documents. Overall, the theory is that you > could speed up > database retrieval incredibly if you did not have to join tables > constantly to retrieve structured data. So many programs > are written > to import and export tabular query results to and from XML that it > seems like somewhat of a useless step. Why not just store entire > structured documents as single entities and retrieve whole > or partial > documents with simple SQL queries? This is the goal of the dbXML > project. The project is only a little more than one week old and is > actively looking for talented volunteer contributors. > http://www.dbxml.org They are looking for help. Maybe we can kill two birds with one stone here. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ _______________________________________________ pipet-devel maillist - pipet-devel@bioinformatics.org http://bioinformatics.org/mailman/listinfo/pipet-devel From gvd at redpoll.pharmacy.ualberta.ca Mon Jul 26 15:51:02 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] Re: Web Page Update References: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca> <379C38B3.222E07B6@bc.edu> Message-ID: <379CBC25.54934859@redpoll.pharmacy.ualberta.ca> J.W. Bizzaro wrote: > > > I like the title and the background. The background looks like a Bowie Poag > image; is it? It most definitely is-- the latest from the Redmond Invasion Tour. > I don't think the menu area color (robin's egg?) matches the > background though. Oh i know.. I'll make something nicer looking as things progress. > BTW, did you catch the tag that goes in the body? > The news program actually generates index.shtml from index.template. > goes in index.template. My design proposal for the pages is to use php to create a shell file. The file will "include" the header (logo, background image, etc.) from a standard file. The Menu will be generated dynamically from a php script (using catalog information included in each individual web page) and placed into the menu table, which can be on the right or left. The main text will again be grabbed from a file, so if i grab index.shtml, which is generated from index.template using (what news proggy are you using?), the most recently generated index.shtml will always appear in the main panel. Im making use of cascading style sheets to format the web pages, so once we have a nice looking template page, applying the style to the existing pages should be a snap. --Gary From bizzaro at bc.edu Mon Jul 26 18:07:27 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] Re: Web Page Update References: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca> <379C38B3.222E07B6@bc.edu> <379CBC25.54934859@redpoll.pharmacy.ualberta.ca> Message-ID: <379CDC1F.9B6011F1@bc.edu> Gary Van Domselaar wrote: > > > I don't think the menu area color (robin's egg?) matches the > > background though. > > Oh i know.. I'll make something nicer looking as things progress. BTW, you probably noticed that I have a different background for each page. The way I put the text in a white table in the middle of the page allows us to use any busy pattern for the background around it. The effect is rather like a window on a computer desktop. I was wondering if we could have a randomly selected background. Perhaps PHP can do this? Also, I am a bit fond of the "cartoon" theme I was starting with but didn't quite implement. Check out the PyGTools page: http://bioinformatics.org/pygtools/ See how the black outlines make it look a little cartoony? I just needed to make some more drawings. Something to think about. But since you're doing the work, you have the say. > > BTW, did you catch the tag that goes in the body? > > The news program actually generates index.shtml from index.template. > > goes in index.template. > > My design proposal for the pages is to use php to create a shell file. The file > will "include" the header (logo, background image, etc.) from a standard file. > The Menu will be generated dynamically from a php script (using catalog > information included in each individual web page) and placed into the menu table, > which can be on the right or left. The main text will again be grabbed from a > file, so if i grab index.shtml, which is generated from index.template using (what > news proggy are you using?), the most recently generated index.shtml will always > appear in the main panel. The program is Htnews: http://www.daemon.de/software.html I can specify a "input/template" file and an "output" file; it doesn't matter what they are called. Check out the /etc/htnews-* files on the system. So whatever you want to "grab" the main text from, we can specify that as the output file, which will come from a template file. It doesn't have to be named the way it is now. > Im making use of cascading style sheets to format the web pages, so once we have a > nice looking template page, applying the style to the existing pages should be a > snap. Good. I hope I can follow all the new additions :-) Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Mon Jul 26 18:54:42 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] workspace work Message-ID: <379CE732.4B1930F1@bc.edu> Locians, Just to update you on the progress of programming Loci, there IS work being done on the Workspace. I've been adding some versatility to the system. For example, each locus can now have multiple inputs and outputs, whereas before there was only one input per locus. I think each locus will have to specify all of the inputs and outputs at the onset, and they'll be represented by open/broken lines. The effect is a bit like placing a "bug" or little critter on the Workspace, because the lines radiating from a geometric shape look like legs on an insect. And the legs of one bug can be connected to another: output is connected to input. Unconnected legs mean some information is missing or the next step is unspecified, and this will likely mean the Workflow Diagram won't..."flow". It's a good visual indicator anyway. Importantly, multiple inputs allow us to have some complex control structures, such as loops, which will make for a very powerful data processing system. I should have a snapshot and a screenshot in a few days. Cheers. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Wed Jul 28 23:12:50 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:45 2006 Subject: [Pipet Devel] an historical diversion Message-ID: <379FC6B2.AACBDD60@bc.edu> Greetings. Since graphical user interfaces are of some importance to this project and a special interest of mine, I thought I'd share a couple pics I came across today. If you are familiar with the history of personal computers, you know the importance of the work done by Xerox. If you are not, you may be surprised that Apple did NOT invent the GUI. It is in fact well known that the Macintosh (and the Lisa) GUI's were "ripped off" from the Xerox Alto. Here is a pic of the Alto from circa late-1970's (yes, the 70's): http://www.best.com/~curbow/xerox/alto.jpg A sobering picture is that of the Xerox Star, which was introduced in 1981, 18 years ago!!! http://www.best.com/~curbow/xerox/1/p10-lg.jpg And of some interest to us, here is a picture of the Xerox Elixir desktop from 1990 (the pic is actually printed on a t-shirt). Notice the "process flow" system, represented by icons connected with lines. Look familiar? http://www.damer.com/pictures/elixir/products/shirt1m.jpg Nine years ago. Hmmm. :-) Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+ From bizzaro at bc.edu Fri Jul 30 11:55:51 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] Thomas Junier joins! Message-ID: <37A1CB07.140CBE73@bc.edu> This is Thomas's reply to my message. He will be joining the project by helping develop a model for translators/filters (programs that convert data from one format to another). Recall that he and Philipp Bucher developed SEView. Jeff -------------- next part -------------- An embedded message was scrubbed... From: Thomas Junier Subject: Re: The Loci Project Date: Fri, 30 Jul 1999 13:19:53 +0200 Size: 3913 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990730/7ee388fc/attachment.mht From bizzaro at bc.edu Sat Jul 31 18:26:47 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Fri Feb 10 19:18:46 2006 Subject: [Pipet Devel] snapshots directory Message-ID: <37A37827.3DA8DD1A@bc.edu> My fellow Locians, We'll be placing all development snapshots for Loci in a new Web directory on the server: http://bioinformatics.org/loci/download/snapshots/ This will give you a listing of all the snapshots available. Adios. Jeff -- +------------------------------------+ | | | J.W. Bizzaro | | jeff@bioinformatics.org | | | | THE OPEN COLLABORATORY | | FOR MOLECULAR BIOINFORMATICS | | | | http://bioinformatics.org/ | | | +------------------------------------+