From valj01 at gel.usherb.ca Wed May 2 23:32:14 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:39:17 2006 Subject: [Pipet Users] Overflow 0.4.2 released Message-ID: <3AF0D13E.89BD081B@gel.usherb.ca> Hi, Just to let you know that I just released Overflow 0.4.2. This release improves Overflow portability. It should now compile without change on Linux, Solaris (x86 at least) and FreeBSD with any GNU compiler between egcs 1.1.2 and the gcc3 pre-releases. Also, for developers, a new config tool: overflow-config, that works in the same way as gnome-config/gtk-config. You can download Overflow 0.4.1 at: http://sourceforge.net/project/showfiles.php?group_id=590 The web page is always at: http://freespeech.sourceforge.net/overflow.html Enjoy, Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Thu May 3 00:07:51 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:17 2006 Subject: [Pipet Users] SRS Message-ID: <3AF0D997.CB4DF5EE@bioinformatics.org> Here's another one very similar to Piper, although it is probably meant more for database integration than for application integration: http://www.lionbioscience.com/htm/c_1/bereich_index.php4?section=c_1_1 Check out this screenshot and note the dots in the center of the links, eerily like Pied/Piper's: http://www.lionbioscience.com/img/c_1/c111_big.gif The funny thing is, this is a bioinformatics application, and the company now employs Peter Rice, who, some may remember, was the project leader of EMBOSS and a regular correspondent on the TULIP (the orginal name for the Pied/Piper UI) mailing list. But of course he started working there before any code was written for TULIP, so the similarities are a coincidence. Cheers. Jeff From d.bain at acbdglobal.com Wed May 9 03:57:16 2001 From: d.bain at acbdglobal.com (David S Bain) Date: Fri Feb 10 19:39:17 2006 Subject: [Pipet Users] Peer-2-Peer Event Message-ID: <00c401c0d85d$aac88500$3201a8c0@b> Skipped content of type multipart/alternative-------------- next part -------------- From jeff at bioinformatics.org Thu May 10 18:20:43 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] [Fwd: natural language processing] Message-ID: <3AFB143B.2FDAA427@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: Jeffrey Chang Subject: Re: natural language processing Date: Thu, 10 May 2001 15:08:59 -0700 Size: 4350 Url: http://bioinformatics.org/pipermail/pipet-users/attachments/20010510/a286b487/attachment.mht From Nicolas.Chauvat at logilab.fr Fri May 11 05:10:15 2001 From: Nicolas.Chauvat at logilab.fr (Nicolas Chauvat) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] [Fwd: natural language processing] In-Reply-To: <3AFB143B.2FDAA427@bioinformatics.org> Message-ID: Dear Pipers, We're in the process of implementing some NLP/U/G capabilities in Narval as we are considering setting up a Narval-powered chat-bot demonstration for the upcoming BotShow in Paris. We doing the "real" stuff, not template-matching. We're planning on contributing some (if not all) of it to the ever-growing GPL'd software heap, so I'll keep you updated. BTW, would any of you guys with some (a lot) of free time be interested in participating to the implementation ? -- Nicolas Chauvat http://www.logilab.com - "Mais o? est donc Ornicar ?" - LOGILAB, Paris (France) From jeff at bioinformatics.org Mon May 14 19:01:54 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] [Fwd: piper] Message-ID: <3B0063E2.D2BD1945@bioinformatics.org> This is from the developer of SEAL, a suit of programs from NCBI. Jeff -------------- next part -------------- An embedded message was scrubbed... From: Roland Walker Subject: piper Date: Mon, 14 May 2001 18:18:06 -0400 Size: 2375 Url: http://bioinformatics.org/pipermail/pipet-users/attachments/20010514/734946ce/attachment.mht From jeff at bioinformatics.org Mon May 14 19:10:39 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Re: piper References: <20010514181806.D11178@ncbi.nlm.nih.gov> Message-ID: <3B0065EF.8A77BE5@bioinformatics.org> Roland Walker wrote: > > I refer you, as I refer everyone who works on such things, to a truly > great and completely unknown piece of software called Praxim. It was > a replacement for the Program Manager that ran under Windows 3.1. > Praxim combined many of the best aspects of CLI and GUI, allowing > operations such as "select all *.txt files but one" as easy to do as > to say. I haven't heard of it. > The company that made it is long dead. Perhaps that is why I haven't heard of it ;-) > I'll mail a copy to > anyone who is interested, but it doesn't work under Windows 95 and > above. Great, send it on over. I'd love to take a look. > I did bookmark piper but I'm very busy (writing up) just now. I'll get > around to giving it a whirl one of these evenings. I take it I should > get the CVS sources and not bother with the tarball on ftp. The tarballs are made from CVS every night. Also, I have to warn you that Piper is alpha-quality right now, and there are some heavy dependencies. We're working on this though. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Mon May 14 19:14:05 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] [Fwd: piper] References: <3B0063E2.D2BD1945@bioinformatics.org> Message-ID: <3B0066BD.98E051A4@bioinformatics.org> "J.W. Bizzaro" wrote: > > This is from the developer of SEAL, a suit of programs from NCBI. ^SEALS ^suite http://www.ncbi.nlm.nih.gov/CBBresearch/Walker/SEALS/index.html Jeff From jeff at bioinformatics.org Mon May 14 19:39:29 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Re: [nocat] SEALS References: <3B002BE4.E8C3B3F8@bioinformatics.org> <20010514153357.J24997@ncbi.nlm.nih.gov> <3B004523.E16B680@bioinformatics.org> <20010514180539.C11178@ncbi.nlm.nih.gov> Message-ID: <3B006CB1.F5349766@bioinformatics.org> Roland Walker wrote: > > If there is some format you need to export > command-line options, I'd be glad to support it. When CLI programs are piped together, in Piper or elsewhere, they're something like linked libraries: whoever or whatever does the linking needs to know something about the I/O parameters. The problem is, CLI programs don't provide that information prior to execution. They *DO* however have human-readable help output (by typing the --help or -h flag). In Piper, programs can be wrapped/ported by hand. But we'd like to automate the process, and probably the best way to do this would be to parse the help output. There seems to be some semblence of a standard, when you look at the output, but I don't believe that there is any. Anyway, if we find the least common denominator, we may try promoting it for CLI programs. Unless someone can think of a better way. We've also considered parsing man files and source code. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From walker at ncbi.nlm.nih.gov Mon May 14 20:49:40 2001 From: walker at ncbi.nlm.nih.gov (Roland Walker) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] making more CLI programs Piper-compliant In-Reply-To: <3B006CB1.F5349766@bioinformatics.org>; from jeff@bioinformatics.org on Mon, May 14, 2001 at 11:39:29PM +0000 References: <3B002BE4.E8C3B3F8@bioinformatics.org> <20010514153357.J24997@ncbi.nlm.nih.gov> <3B004523.E16B680@bioinformatics.org> <20010514180539.C11178@ncbi.nlm.nih.gov> <3B006CB1.F5349766@bioinformatics.org> Message-ID: <20010514204940.C14480@ncbi.nlm.nih.gov> [jeff writes] > > If there is some format you need to export > > command-line options, I'd be glad to support it. > > When CLI programs are piped together, in Piper or elsewhere, they're something > like linked libraries: whoever or whatever does the linking needs to know > something about the I/O parameters. The problem is, CLI programs don't > provide that information prior to execution. They *DO* however have > human-readable help output (by typing the --help or -h flag). In Piper, > programs can be wrapped/ported by hand. But we'd like to automate the > process, and probably the best way to do this would be to parse the help > output. There seems to be some semblence of a standard, when you look at the > output, but I don't believe that there is any. Anyway, if we find the least > common denominator, we may try promoting it for CLI programs. > > Unless someone can think of a better way. We've also considered parsing man > files and source code. There is absolutely a better way. Don't parse the help output. This is harder than doing things the nominally hard way. 1 First, you must wrap some CLI elements by hand. This is needed to get started, yes? and you are doing it already, yes? Wrapping basically means standardizing the handling of STDIN, STDOUT, and STDERR, trying to tame buffering, and providing some formalization of the options. This is not too hard; it's my own stock in trade. 2 Provide an _easy_ way for CLI authors to export options, making makes their programs drop-in elements for you. This means not writing yet another standard, which authors will just ignore, but giving authors the needed code. This is not as hard as it seems. One can write a perl module that reads the simple argument spec given in Getopt::Long, and translates it to Piper-spec. 4 out of 10 interesting programs are written in perl already. 8 out of 10 coders are amateur perl coders. 8 out of 10 amateur perl coders have used Getopt::Long. So conquer Getopt::Long. You will get many elements. Then conquer the PPT (Perl Power Tools) project, which duplicates most basic Unix commands. You won't have to conquer SEALS, as I'll just give it to you. I assume you have written an XML spec to define the options? That's what I would have done if XML was around when I started my thing. Give me your spec and a give me a couple of hours, and I can give you a Getopt::Piper that is drop-in compatible with Getopt::Long. I'm not claiming this is perfect, just useful as heck. Cram new programs in to your system as hard as you can. If you reach a certain critical mass, all kinds of stuff will start to come your way. There are dozens of scripts here at NCBI that use the same library for argument processing. For some reason argument processing and CLI usability is an obsessive interest of mine. Anyway, I build a data structure that holds more than anyone could want to know about processing the options for a CLI script. Then I like to do more with that than merely process the options. For instance, each script can generate programmable completions for tcsh based on its expected arguments: [thorin] {/home/walker/downloads:1751} gi2fasta -tcsh_completions complete gi2fasta {n,c}/{-,--,}{index_method,master_db,http_server}{=,}/x:""/ {n,c}/{-,--,}{hint,only_hint}{=,}/x:""/ {n,c}/{-,--,}{dollop,timeout,tries}{=,}/x:""/ \ c/-{-,}/"(index_method= master_db= http_server= hint= only_hint= dollop= timeout= tries= save append delete feedback defline_as_hint swallow_failures secure insist show_spacers no_save no_append no_delete no_feedback no_defline_as_hint no_swallow_failures no_secure no_insist no_show_spacers argsets help version tcsh_completions)"/ 'c/@/`argsets --terse $:0`/' This lets you do [thorin] {/home/walker/downloads:1751} gi2fasta -htt [thorin] {/home/walker/downloads:1751} gi2fasta -http_server= and generally makes -long_option_names more tolerable. I'd generate bash and zsh completions too if I had the time; I'd make the time if someone had the need. Once, someone at NCBI wanted to drive SEALS scripts via CGI off of a separate GUI. We said, no problem, just show us the what kind of spec you want to see for the options. The SEALS side must have taken about a day. So to you Piperians, I say, show me your spec, I'll throw it into the main SEALS library so that all scripts can be queried, say, like this gi2fasta -piper_options to return your spec, giving you a sizable wad of new CLI elements for your system. There is certainly some duplication, but duplication can even be good. I am not into the idea of a single perfect system, or a single best way, but rather in opening up new ways which are new paths for users to wander. Furthermore, you may have our module if you find it useful. I'd say the module is wonderful, though idiosyncratic. Fixing it for general use means mostly indenting and deleting. In addition, the research side at the NCBI is a powerfully active testbed. If you could get folks using Piper here, you would get a _lot_ of feedback. Think critical mass. So I think that the only hitch between us and a world of excitement is the lamentable lack of a packaging system that can tame the SEALS monster. We have multiple revisions we need to reconcile, and tangles of code that we rather urgently need to clean up and push out the door in some usable form. Please feel free to write to Janos Murvai at murvai@ncbi.nlm.nih.gov if you are interested in the status of the SEALS packaging project. R From walker at ncbi.nlm.nih.gov Tue May 15 02:57:03 2001 From: walker at ncbi.nlm.nih.gov (Roland Walker) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Re: piper In-Reply-To: <3B0065EF.8A77BE5@bioinformatics.org>; from jeff@bioinformatics.org on Mon, May 14, 2001 at 11:10:39PM +0000 References: <20010514181806.D11178@ncbi.nlm.nih.gov> <3B0065EF.8A77BE5@bioinformatics.org> Message-ID: <20010515025703.C20754@ncbi.nlm.nih.gov> [jeff writes] > Roland Walker wrote: > > I refer you, as I refer everyone who works on such things, to a truly > > great and completely unknown piece of software called Praxim. It was > > Great, send it on over. I'd love to take a look. I'll send a URL to you under separate cover. R From Nicolas.Chauvat at logilab.fr Tue May 15 04:00:01 2001 From: Nicolas.Chauvat at logilab.fr (Nicolas Chauvat) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] making more CLI programs Piper-compliant In-Reply-To: <20010514204940.C14480@ncbi.nlm.nih.gov> Message-ID: > One can write a perl module that reads the simple argument spec > given in Getopt::Long, and translates it to Piper-spec. 4 out of > 10 interesting programs are written in perl already. 8 out of 10 > coders are amateur perl coders. 8 out of 10 amateur perl coders > have used Getopt::Long. So conquer Getopt::Long. You will get > many elements. Then conquer the PPT (Perl Power Tools) project, > which duplicates most basic Unix commands. And 8 out of 10 sensible perl coders have been considering moving to Python for the past year (at least) ;-) BTW, I like your description of SEALS and thought about doing exactly what you describe to automate cli tools wrapping... but for Narval. Glad to see Narval, Piper's relations have so much in common. I can't wait to actually find time to get them to work together, they'd have a lot to gain from it! -- Nicolas Chauvat http://www.logilab.com - "Mais o? est donc Ornicar ?" - LOGILAB, Paris (France) From walker at ncbi.nlm.nih.gov Tue May 15 04:22:47 2001 From: walker at ncbi.nlm.nih.gov (Roland Walker) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] making more CLI programs Piper-compliant In-Reply-To: ; from Nicolas.Chauvat@logilab.fr on Tue, May 15, 2001 at 10:00:01AM +0200 References: <20010514204940.C14480@ncbi.nlm.nih.gov> Message-ID: <20010515042247.A27645@ncbi.nlm.nih.gov> [Nicolas.Chauvat writes] > And 8 out of 10 sensible perl coders have been considering moving to > Python for the past year (at least) ;-) Really? I'm not sensible at all, so sensibilities don't sway me. I do Perl. And Perl is here to stay; we should work with it. I think Python is neat. And Python is here to stay; we should work with it. R From valj01 at gel.usherb.ca Tue May 22 00:39:29 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Overflow 0.4.3 released Message-ID: <3B09ED81.E4283203@gel.usherb.ca> Just letting you know that version 0.4.3 of Overflow (http://freespeech.sourceforge.net/overflow.html) has been released. Download location is as usual: http://sourceforge.net/project/showfiles.php?group_id=590 The main point in this release is that it allows to use the speaker verification prototype I just made available at: ftp://freespeech.sourceforge.net/pub/freespeech/speaker_verification-0.0.1.tgz Otherwise, it shouldn't break source compatibility with previous releases. Have fun! Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Tue May 22 10:16:11 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] [Fwd: OiBC-2001] Message-ID: <3B0A74AB.B0B53809@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: W_David_Benton@sbphrd.com Subject: OiBC-2001 Date: Tue, 22 May 2001 09:55:48 -0400 Size: 2569 Url: http://bioinformatics.org/pipermail/pipet-users/attachments/20010522/86bf8cd4/attachment.mht From jeff at bioinformatics.org Tue May 22 11:07:49 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Re: making more CLI programs Piper-compliant References: <3B002BE4.E8C3B3F8@bioinformatics.org> <20010514153357.J24997@ncbi.nlm.nih.gov> <3B004523.E16B680@bioinformatics.org> <20010514180539.C11178@ncbi.nlm.nih.gov> <3B006CB1.F5349766@bioinformatics.org> <20010514204940.C14480@ncbi.nlm.nih.gov> Message-ID: <3B0A80C5.CD313737@bioinformatics.org> (late reply) Roland Walker wrote: > > There is absolutely a better way. Don't parse the help output. This > is harder than doing things the nominally hard way. > > 1 First, you must wrap some CLI elements by hand. This is needed > to get started, yes? and you are doing it already, yes? Wrapping > basically means standardizing the handling of STDIN, STDOUT, > and STDERR, trying to tame buffering, and providing some > formalization of the options. This is not too hard; it's my own > stock in trade. Actually, we've come up with a way to do the wrapping using connect-the-dots: http://www.bioinformatics.org/piper/documentation/command-compilation.html Sure, programmers will find it simpler to write one by hand, but perhaps non-programmers will find it usable. In any case, it's been an academic excercise to see how many things can be done using connect-the-dots. > 2 Provide an _easy_ way for CLI authors to export options, making > makes their programs drop-in elements for you. This means not > writing yet another standard, which authors will just ignore, but > giving authors the needed code. This is not as hard as it seems. Is there ANY standard out there? Can you provide us with an example? > You won't have to conquer SEALS, as I'll just give it to you. Great. > I assume you have written an XML spec to define the options? That's > what I would have done if XML was around when I started my thing. Sort-of. It's a long story. Basically, we already *CAN* define options using XML, but that is due to the dataflow nature of Piper. We should probably come up with clear specs though. > Give me your spec and a give me a couple of hours, and I can give you > a Getopt::Piper that is drop-in compatible with Getopt::Long. Super. > I'm not claiming this is perfect, just useful as heck. Cram new > programs in to your system as hard as you can. If you reach a certain > critical mass, all kinds of stuff will start to come your way. That's our motto :-) > There are dozens of scripts here at NCBI that use the same library for > argument processing. For some reason argument processing and CLI > usability is an obsessive interest of mine. Anyway, I build a data > structure that holds more than anyone could want to know about > processing the options for a CLI script. You're the man to talk to about this then! > Then I like to do more with > that than merely process the options. For instance, each script can > generate programmable completions for tcsh based on its expected > arguments: For Piper, grepping what the program needs for parameters is more important than grepping what the parameters do. Piper is "dumb" that way: it doesn't care what data passes through it; it's the responsibility of the node/program to deal with it (although we'd like to help the user make the right connections). > So to you Piperians, I say, show me your spec, I'll throw it into > the main SEALS library so that all scripts can be queried, say, > like this > > gi2fasta -piper_options > > to return your spec, giving you a sizable wad of new CLI elements > for your system. Again, I'd be interested in seeing what others have come up with and if there may be some sort of a standard approach. We'd be interested in promoting a standard (say for GNU programs). > There is certainly some duplication, but duplication > can even be good. I am not into the idea of a single perfect > system, or a single best way, but rather in opening up new ways > which are new paths for users to wander. The old standards vs. freedom to innovate argument :-) > Furthermore, you may have our module if you find it useful. I'd say > the module is wonderful, though idiosyncratic. Fixing it for general > use means mostly indenting and deleting. Thanks. > In addition, the research side at the NCBI is a powerfully active > testbed. If you could get folks using Piper here, you would get > a _lot_ of feedback. > > Think critical mass. >From the bioinformatics side of Piper development, I can say that it would be a Great Thing to have NCBI involved :-) > So I think that the only hitch between us and a world of excitement > is the lamentable lack of a packaging system that can tame the SEALS > monster. We have multiple revisions we need to reconcile, and > tangles of code that we rather urgently need to clean up and push > out the door in some usable form. Are you thinking along the line of RPM, Deb, or CPAN? Thanks for the message. It was very helpful. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From walker at ncbi.nlm.nih.gov Tue May 22 16:25:57 2001 From: walker at ncbi.nlm.nih.gov (Roland Walker) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Re: making more CLI programs Piper-compliant In-Reply-To: <3B0A80C5.CD313737@bioinformatics.org>; from jeff@bioinformatics.org on Tue, May 22, 2001 at 03:07:49PM +0000 References: <3B002BE4.E8C3B3F8@bioinformatics.org> <20010514153357.J24997@ncbi.nlm.nih.gov> <3B004523.E16B680@bioinformatics.org> <20010514180539.C11178@ncbi.nlm.nih.gov> <3B006CB1.F5349766@bioinformatics.org> <20010514204940.C14480@ncbi.nlm.nih.gov> <3B0A80C5.CD313737@bioinformatics.org> Message-ID: <20010522162556.A27710@ncbi.nlm.nih.gov> [jeff writes] > Roland Walker wrote: > > There is absolutely a better way. Don't parse the help output. This [snip] > Actually, we've come up with a way to do the wrapping using connect-the-dots: > > http://www.bioinformatics.org/piper/documentation/command-compilation.html > > Sure, programmers will find it simpler to write one by hand, but perhaps > non-programmers will find it usable. In any case, it's been an academic > excercise to see how many things can be done using connect-the-dots. I do find the connect-the-dots hard. Remember that non-programmers find it easiest of all to just find a programmer to do it. It all comes down to settling on a spec. I don't know about getting FSF to accept your spec; they can be arbitrary and obtuse. But perhaps the XML buzzword would make people happy enough to follow it. Such a thing certainly needs to be done. With all the work that goes into CORBA and DCOP and the like, you'd think someone would formulate a simple standard for querying a CLI program for its options. Though I think that the principle benefit would be improving shells, not eliminating them. Anyway, if do you get a spec to me, I will support it, as I think you are working on some cool ideas. > > So I think that the only hitch between us and a world of excitement > > is the lamentable lack of a packaging system that can tame the SEALS > > monster. We have multiple revisions we need to reconcile, and > > tangles of code that we rather urgently need to clean up and push > > out the door in some usable form. > > Are you thinking along the line of RPM, Deb, or CPAN? We need to make CPAN-style packages first. And it suddenly looks like that project is on hold again for lack of manpower. R PS I wasn't able to get Piper to compile on my Solaris box. I'll try a later build, maybe on my Linux box, and give you some feedback. From andy.elvey at paradise.net.nz Wed May 23 03:39:06 2001 From: andy.elvey at paradise.net.nz (Andy Elvey) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] A (possibly ! ) useful resource - Blue Orca Message-ID: <001601c0e35b$7372b400$95414fcb@andyelve> Hi all . Just thought I'd mention another open-source project which is using pipelining (somewhat similarly to Piper). This is the package called "Blue Orca" - http://pyrite.cfas.washington.edu/orca/ . This is a Java-based package. A brief quote from its website - " The Orca Framework separates different aspects of data processing and rendering into segments of a pipeline. " This project seems to emphasize data visualisation more than the pipelining side of things, but anyway - it may be a useful resource for ideas! Looks like a very nice package .... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://bioinformatics.org/pipermail/pipet-users/attachments/20010523/3b761732/attachment.html From jeff at bioinformatics.org Wed May 23 04:33:54 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] A (possibly ! ) useful resource - Blue Orca References: <001601c0e35b$7372b400$95414fcb@andyelve> Message-ID: <3B0B75F2.B4149AF1@bioinformatics.org> > Andy Elvey wrote: > > http://pyrite.cfas.washington.edu/orca/ Thanks, Andy! I haven't seen that one before. It does seem to be along the line of OpenDX, Vector NTI, Khoros, etc., in that it is used for data visualization. I even see some biology apps in the examples. I've been wanting to target Piper, at least initially, at command-line programs, providing a "better UNIX GUI" by allowing the UNIX paradigm (do complex things by connecting small, simple tools) and programs to work in a completely graphical environment. And of course across a network. This is *MY* ambition anyway (it may not be Jarl's or Jean-Marc's), and this type of application does seem to be less common than more traditional data vis/flow and visual programming applications, using specialized nodes. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From Alexandre.Fayolle at logilab.fr Wed May 23 05:59:11 2001 From: Alexandre.Fayolle at logilab.fr (Alexandre Fayolle) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] ANN: Narval 1.0 Message-ID: Logilab (www.logilab.com) announces the release of Narval 1.0 GPL'd Intelligent Personnal Assistant Framework http://www.logilab.org/narval News ---- The engine is now stable as it has been working nicely for the past three months. It's also much faster. The Horn GUI features lots of usability improvements. The infopal application (available separately) is now usable. Description ----------- Narval is a framework (language + interpreter + GUI/IDE) dedicated to the setting up of intelligent personal assistants (IPAs). An Intelligent Personal Assitant is a companion that will help you in your daily work in the information world. It runs on your machine or on a remote server, and you can communicate with it via all standard means (email, web, telnet, phone, specific GUI, etc). It executes recipes (sequences of actions) you wrote, to perform a wide range of tasks, such as prepare your morning newspaper, help you surf the web by filtering out junk ads, keep searching the web day after day for things you want, participe in on-line auctions, learn you interests and bring you back valuable information, take care of repetitive chores, answer e-mail, negociate the date and time of a meeting, and much more... It is easy to extend the built in action library by writing new actions in Python. Infopal, your information pal, is a Narval application that implements part of the above, but Narval makes it easy for you to set up new assistants. Others applications will soon be available from Logilab. Logilab S.A. is a french company that specializes in the fields of artificial intelligence, knowledge management, data analysis and natural language processing. More info --------- Please see http://www.logilab.org/narval http://www.logilab.com http://www.logilab.fr or contact contact@logilab.fr -- Alexandre Fayolle http://www.logilab.com Narval is the first software agent available as free software (GPL). LOGILAB, Paris (France). From rossini at blindglobe.net Wed May 23 13:00:14 2001 From: rossini at blindglobe.net (A.J. Rossini) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] A (possibly ! ) useful resource - Blue Orca In-Reply-To: "J.W. Bizzaro"'s message of "Wed, 23 May 2001 08:33:54 +0000" References: <001601c0e35b$7372b400$95414fcb@andyelve> <3B0B75F2.B4149AF1@bioinformatics.org> Message-ID: <87u22c3srl.fsf@jeeves.blindglobe.net> >>>>> "JWB" == J W Bizzaro writes: >> Andy Elvey wrote: >> >> http://pyrite.cfas.washington.edu/orca/ JWB> Thanks, Andy! I haven't seen that one before. It does seem JWB> to be along the line of OpenDX, Vector NTI, Khoros, etc., in JWB> that it is used for data visualization. I even see some JWB> biology apps in the examples. And we've been following Piper. Orca's strength is in the pipeline interface, and the weakness is in its Java implementation (well, if you like Java, it's not, but...). The pipeline seems to do fine for moderate sized data, but we are talking high-throughput technologies, so visual summaries are critical. There is a graphical interface (based on the argoUML code) for graphically constructing the visualization. It's semi-stalled right now, but I'll be working more on it (and integration with R, www.r-project.org, a statistics package), in the next few months, as I FINALLY get a chance to code again... (at least that's the plan. This is the Nth time I've thought so, and N-1 prior times I was wrong). best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics UW Biostat/Center for AIDS Research rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------- (friday is unknown) -------- FHCRC: M--W : 206-667-7025 (fax=4812)|Voicemail is pretty sketchy CFAR: ?? : 206-731-3647 (fax=3694)|Email is far better than phone UW: Th : 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX From rossini at blindglobe.net Wed May 23 13:03:52 2001 From: rossini at blindglobe.net (A.J. Rossini) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] A (possibly ! ) useful resource - Blue Orca In-Reply-To: rossini@blindglobe.net's message of "23 May 2001 10:00:14 -0700" References: <001601c0e35b$7372b400$95414fcb@andyelve> <3B0B75F2.B4149AF1@bioinformatics.org> <87u22c3srl.fsf@jeeves.blindglobe.net> Message-ID: <87lmno3slj.fsf@jeeves.blindglobe.net> >>>>> "AJR" == A J Rossini writes: >>>>> "JWB" == J W Bizzaro writes: >>> Andy Elvey wrote: >>> >>> http://pyrite.cfas.washington.edu/orca/ Actually, http://software.biostat.washington.edu/orca/ best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics UW Biostat/Center for AIDS Research rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------- (friday is unknown) -------- FHCRC: M--W : 206-667-7025 (fax=4812)|Voicemail is pretty sketchy CFAR: ?? : 206-731-3647 (fax=3694)|Email is far better than phone UW: Th : 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX From andy.elvey at paradise.net.nz Fri May 25 03:47:53 2001 From: andy.elvey at paradise.net.nz (Andy Elvey) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Re: Blue Orca References: <200105241600.MAA06952@www.bioinformatics.org> Message-ID: <000e01c0e4ef$02b97880$659a60cb@andyelve> Just thought I'd mention the following URL too (while on the subject of "R" ! ) . http://www.omegahat.org This is an *excellent* site which is centred around R. This site has R interfaces to - * SPlus * Python * Java * XML * Xalan (XSLT ) The "R" core developers are heavily involved in this project as well . Definitely worth bookmarking ..... :-) > Actually, > http://software.biostat.washington.edu/orca/ > > best, > -tony > > > -- > A.J. Rossini Rsrch. Asst. Prof. of Biostatistics > UW Biostat/Center for AIDS Research rossini@u.washington.edu > FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org > -------- (friday is unknown) -------- > FHCRC: M--W : 206-667-7025 (fax=4812)|Voicemail is pretty sketchy > CFAR: ?? : 206-731-3647 (fax=3694)|Email is far better than phone > UW: Th : 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX > > > > --__--__-- > > _______________________________________________ > pipet-users maillist - pipet-users@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/pipet-users > > > --__--__---- > > End of pipet-users Digest >