Re: Debian for Systems Biology
On Sun, 29 Jan 2006 10:24:09 +0900 Charles Plessy [EMAIL PROTECTED] wrote: But I think that the real problem is that most academic software is non-free, as it often mentions Do not make money with our work, or share it with us. Thus splitting debian-med would result in dilluting sparse packages into something not really useful. That's likely true. It's also true that things are slowly changing... and we can run in that direction ;-) Then, why don't we try to gather more packages related to computational biology, and when a critical mass is reached, we could discuss with Andreas and the debian-med people to ask if a renaming of the project into something like debian-biomed would make sense? I told about software that often concerns mathematics and biochemistry etc. more than medicine, does make it sense that all what's biology-related become part of debian-med/bio-med, included e.g. industrial biotech? Well, it perhaps make some sense until the mass of free software in these fields doesn't exceed one threshold... So, anyway, I'm ready to contribute to gather packages and packageable software related to computational biology, biophysics, bioinformatics, systems biology etc. Why don't we create a very simple wiki page? I can help for testing or translating packages (a surprisingly big number of computational biologists are very uncomfortable with english). If there is a lot of packaging to do, well, you would have to teach me... and me too! I can help in the same things, And I'll try soon to make some unofficial packages. Charles, if you would to contact me you can see below ;-) -- Luca Brivio Jabber: [EMAIL PROTECTED] [EMAIL PROTECTED] ICQ:234046116 MSN IM: [EMAIL PROTECTED] -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian for Systems Biology
On 1/29/06, Charles Plessy [EMAIL PROTECTED] wrote: Hi list. Luca and I chatted briefly on jabber, and we are about to open a wiki page on www.open-bio.org, in which we will list packages in molecular biology and systems biology which could make it into debian, and see how we can help it to happen. Why not use the already-existing Debian wiki page at http://wiki.debian.org/DebianScienceBiology ? (For those who aren't aware, you don't need to be a Debian Developer to edit the wiki; you just need to create an account there for yourself.) regards, -- Kevin B. McCarty [EMAIL PROTECTED] Physics Department WWW: http://www.princeton.edu/~kmccarty/Princeton University GPG: public key ID 4F83C751 Princeton, NJ 08544
Re: Debian for Systems Biology
On Sun, 29 Jan 2006 10:32:30 -0500 Kevin B. McCarty [EMAIL PROTECTED] wrote: Why not use the already-existing Debian wiki page at http://wiki.debian.org/DebianScienceBiology ? (For those who aren't aware, you don't need to be a Debian Developer to edit the wiki; you just need to create an account there for yourself.) The Debian wiki homepage says: This wiki is a support and documentation resource for the Debian project. So we'd supposed it wasn't for development purposes... However, I think we'll consider whether use that. -- Luca Brivio Jabber: [EMAIL PROTECTED] [EMAIL PROTECTED] ICQ:234046116 MSN IM: [EMAIL PROTECTED] -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian for Systems Biology
On 1/29/06, Luca Brivio [EMAIL PROTECTED] wrote: On Sun, 29 Jan 2006 10:32:30 -0500 Kevin B. McCarty [EMAIL PROTECTED] wrote: Why not use the already-existing Debian wiki page at http://wiki.debian.org/DebianScienceBiology ? (For those who aren't aware, you don't need to be a Debian Developer to edit the wiki; you just need to create an account there for yourself.) The Debian wiki homepage says: This wiki is a support and documentation resource for the Debian project. So we'd supposed it wasn't for development purposes... No need to worry -- if you take a look at http://wiki.debian.org/RecentChanges it is pretty clear that one of its primary uses is inter-developer communication. Actually, let me go add that to the front page :-) However, I think we'll consider whether use that. If you decide not to, please do at least add a link from the DebianScienceBiology change to your own wiki. best regards, -- Kevin B. McCarty [EMAIL PROTECTED] Physics Department WWW: http://www.princeton.edu/~kmccarty/Princeton University GPG: public key ID 4F83C751 Princeton, NJ 08544
Re: Debian for Systems Biology
On Sun, 29 Jan 2006, Luca Brivio wrote: On Sun, 29 Jan 2006 10:24:09 +0900 Charles Plessy [EMAIL PROTECTED] wrote: But I think that the real problem is that most academic software is non-free, as it often mentions Do not make money with our work, or share it with us. Thus splitting debian-med would result in dilluting sparse packages into something not really useful. That's likely true. It's also true that things are slowly changing... and we can run in that direction ;-) Well, IMHO it makes no sense to split up Debian-Med before something else covers the problem we solve. IMHO the Custom Debian Distribution idea (Debian-Med is one of the CDDs see http://people.debian.org/~tille/cdd/ ) is about grouping sunsets of Debian into practical pieces of software that a certain group of users needs. There might be intersection inbetween these subsets which means if there would be an imaginary Debian-Science CDD or a Debian-Bio CDD that some packages could be included via the meta packages in more than one CDD. So if a biologist installs a imaginary meta package 'bio-genetics' it might perfectly be possible that a user working in medical care installs the 'med-bio' package (which just exists!) and gets nearly the same set of packages on his box. Then, why don't we try to gather more packages related to computational biology, and when a critical mass is reached, we could discuss with Andreas and the debian-med people to ask if a renaming of the project into something like debian-biomed would make sense? I told about software that often concerns mathematics and biochemistry etc. more than medicine, does make it sense that all what's biology-related become part of debian-med/bio-med, included e.g. industrial biotech? Well, it perhaps make some sense until the mass of free software in these fields doesn't exceed one threshold... So just start caring for an optimal solution for biologists before you try to start arguing how we can stop users in medical care from easily installing some biology related software, right. It is not the problem of Debian-Med that there is no other help for biologists that they get some comfort by installing apackage that starts with 'med-'. Why don't we create a very simple wiki page? My personal experience of Wiki pages in small projects is that they are not really maintained. That's why I save my personal time and do not create such a page. If you think differently - just start the page. I will not stop you. ;-)) I can help for testing or translating packages (a surprisingly big number of computational biologists are very uncomfortable with english). If there is a lot of packaging to do, well, you would have to teach me... and me too! I can help in the same things, And I'll try soon to make some unofficial packages. This would be great. You can count on my support in sponsoring these packages. Charles, if you would to contact me you can see below ;-) Just use the mailing list here. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian for Systems Biology
On Sun, 29 Jan 2006, Kevin B. McCarty wrote: Luca and I chatted briefly on jabber, and we are about to open a wiki page on www.open-bio.org, in which we will list packages in molecular biology and systems biology which could make it into debian, and see how we can help it to happen. Why not use the already-existing Debian wiki page at http://wiki.debian.org/DebianScienceBiology ? (For those who aren't aware, you don't need to be a Debian Developer to edit the wiki; you just need to create an account there for yourself.) Ahh, this is also a reasonable idea: We could just use this wiki as kind of a TODO-list for updates of http://www.debian.org/devel/debian-med/microbio everybody could add projects to this list after checking the page above. This would probably a nice help for Tobias who cares for the Debian-Med pages. Even better would be if there would be some license information and a short description inside the Wiki. Once it would be moved to the official web pages the Debian-WWW translation team cares for the translation. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian for Systems Biology
On Mon, Jan 30, 2006 at 07:27:13AM +0100, Andreas Tille wrote : Well, several months ago I suggested that we should start building such web pages automatically and started some very basic code (which is far from beeing usable and no chance of continuing this for some further months). The idea is as follows: 1) Obtain the contents of the first part of the web page by parsing Packages.gz file for a list of packages that should be listed on the page. 2) Use ddtp translations for translated pages. (Well, unfortunately the ddtp project is currently in a quite bad state. It was much more usable before the break into the Debian servers in the end of 2003. :-() 3) Build a fake Package.gz file containing the projects that should be included into Debian and into the CDD in question to build the list of projects with inofficial packages or are not yet packaged and use the algorithm from 1) to create the other part of the web page. If we would have such a system every project could easily build the web needed web pages by just compiling a list of projects that should be included. So if the only thing you do not like is the name of the page you could compile your own one by just renaming the list name (that might lead to a page name) and perhaps add or remove some projects. That way we will not double any work but gain maximum flexibility. That sounds nice, but as you say, it requires some preliminary work before doing the core work, which is increasing the number of packages related to biology in debian. Although I warmly welcome anybody who would code this, I will not do it before it becomes that kind of itch which one wants to scratch. In order to create a dynamic, we need some quick results. I want to start with a simple list, with the program name, the purpose, the freedom, a rating of the difficulty to integrate to debian, and the alternatives. Then if we manage to enrich debian of a few packages, we can think about giving some time to building a better infrastructure... [By the way, talking about ddtp, it is a shame that it does not work anymore, because the tranlation of your debian-med pages, which are mostly descripion of packages or prospective packages, generated a lot of translations of descriptions of debian packages! So the people who would like to revive the ddtp will not start with no material.] Also, I wonder how some existing packages could be tweaked. For instance, the search box of firefox can be used to query very relevant databases, such as pubmed.gov or genbank (http://www.ncbi.nlm.nih.gov/Genbank/), You mean mozilla-biofox? Not sure. It seems that biofox is a toolbar with many functionalities. In mozilla-derived browsers, there is a small field right of the url field, from which a google search can be started. Other search engines can be added, including scientific ones. It is less powerful than biofox, but on the other hand is not a plugin, but a built-in fuction that can be configured. But I wonder wether this, and the default bookmarks, can be easily tweaked in a custom debian distribution. Best, -- Charles -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian for Systems Biology
Ciao Luca, Is there anybody interested to packaging software for systems biology? you mean in already packaged software :-) I'm a bioinformatics student, and I noticed nobody within Debian is packaging systems biology-related tools (there is only an old ITP for libsbml). It is mine. I have a quite ok package for a while but have never addressed the soname issue. If you are actively using SBML then please take over. Wouldn't be useful to create a webpage like those at http://www.debian.org/devel/debian-med/? Of course, actually systems biology inherit science more than medicine. debian-science should have its own webpage, shouldn't it? Andreas Tille does a very good and reliable job that takes more time than you might anticipate. In short, No!. A chaotic list with a few interesting tools for the main Debian distribution with their licenses follows. Anyone could surely look better. I experienced the Java bits as tricky. Please go for the packaging of any of these tools that you actively use yourself. Many saluti Steffen -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian for Systems Biology
On Sat, 28 Jan 2006 22:34:47 +0100 (MET) Steffen Möller [EMAIL PROTECTED] wrote: Is there anybody interested to packaging software for systems biology? you mean in already packaged software :-) Already packaged? Which packages? I'm a bioinformatics student, and I noticed nobody within Debian is packaging systems biology-related tools (there is only an old ITP for libsbml). It is mine. I have a quite ok package for a while but have never addressed the soname issue. If you are actively using SBML then please take over. A few weeks ago I just didn't know what SBML is... Wouldn't be useful to create a webpage like those at http://www.debian.org/devel/debian-med/? Of course, actually systems biology inherit science more than medicine. debian-science should have its own webpage, shouldn't it? Andreas Tille does a very good and reliable job that takes more time than you might anticipate. In short, No!. Very good job indeed, but I don't understand what do you mean. A chaotic list with a few interesting tools for the main Debian distribution with their licenses follows. Anyone could surely look better. I experienced the Java bits as tricky. Please go for the packaging of any of these tools that you actively use yourself. It isn't so easy, maybe some day I'll know how to make that. Debian could become the best choice for using and developing bioinformatics software! ;-) -- Luca Brivio Web:? Jabber: [EMAIL PROTECTED] [EMAIL PROTECTED] ICQ:234046116 MSN IM: [EMAIL PROTECTED]
Re: Debian for Systems Biology
On Sat, Jan 28, 2006 at 10:34:47PM +0100, Steffen Möller wrote : Wouldn't be useful to create a webpage like those at http://www.debian.org/devel/debian-med/? Of course, actually systems biology inherit science more than medicine. debian-science should have its own webpage, shouldn't it? Andreas Tille does a very good and reliable job that takes more time than you might anticipate. In short, No!. Hi, On the other hand, the debian-med page lists a lot of software which is only distantly related to medecine, and which would better be described by bioinformatics. I think that it somehow conceals what debian can offer non-M.D. biologists. But I think that the real problem is that most academic software is non-free, as it often mentions Do not make money with our work, or share it with us. Thus splitting debian-med would result in dilluting sparse packages into something not really useful. Then, why don't we try to gather more packages related to computational biology, and when a critical mass is reached, we could discuss with Andreas and the debian-med people to ask if a renaming of the project into something like debian-biomed would make sense? I can help for testing or translating packages (a surprisingly big number of computational biologists are very uncomfortable with english). If there is a lot of packaging to do, well, you would have to teach me... Have a nice day, -- Charles -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
