Re: Random numbers generation
Thomas Walter <[EMAIL PROTECTED]> writes:
> Just for completeness to the random generators mentioned above.
> If your system has '/dev/random'
Before investing in using /dev/random note it can "run out" of
numbers. When generating, one will have to do things like move the
mouse or type.
You can see this yourself by doing:
cat /dev/random | od
("od" is used so you don't corrupt your terminal with all the 8 bit
chars that will be generated).
-Brett.
--
To UNSUBSCRIBE, email to [EMAIL PROTECTED]
with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Random numbers generation
Hi Yannick, On Thu, 2005-12-08 at 21:45, Yannick Patois wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Thomas Walter wrote: > > On Thu, 2005-12-08 at 00:22, Stuart Prescott wrote: > >>The GSL documentation talks a bit about the different generators > >>available and I highly recommend some of the references therein (Park & > >>Miller and L'Ecuyer in particular). > >>http://www.gnu.org/software/gsl/manual/gsl-ref_17.html > > > Just for completeness to the random generators mentioned above. > > If your system has '/dev/random' and/or '/dev/urandom' then you have > > also a good random to read from. This is feed by several non > > deterministic data available on your system. The more usage and traffic > > you have, the better. > > Those random generators have to be avoided, except in very specific > cases as they are not reproducable; there is no way to replay them. > That's the definition of random -- you do not know what's comming next and no chance to repeat. Some random-generator algorithms are very good to show no pattern. Even in a higher dimension space. But true random has no pattern, no matter how long and good you look at. Another try may be a chaotic system, but I do not know. If you want a replay then simply remember the sequence. Or prepare the sequence by anything you want and then feed it into your application. That seems to be the best approach as the using application is independent from source of "random" varying from poor til true. Kind Regards, Thomas -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Packaging and Maintaining
On Thu, 8 Dec 2005, Dirk Eddelbuettel wrote: Andreas' URL to the Debian Med project also had a lot of bio/generics pointers. ... and if you konow something that is missing on this page just write an e-mail to the debian-med list - that's what this list is for. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: [pkg-bioc] Re: Genetics Program
On Thu, 8 Dec 2005, Dirk Eddelbuettel wrote: | http://www.debian.org/devel/debian-med/microbio Nice page(s that I was in fact unaware of. I only need to know your med-* meta packages :) Well, my plan is to build this kind of pages automagically from metapackage dependencies (for the offical packages part) and a database of "future packages" for every CDD using a common toolkit. Unfortunately noone was able to lend me a time travel device to get some extra days for implementing this. I hope you might be able to see the power of CDD ideas for every field of science anyway. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Random numbers generation
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Thomas Walter wrote: > On Thu, 2005-12-08 at 00:22, Stuart Prescott wrote: >>The GSL documentation talks a bit about the different generators >>available and I highly recommend some of the references therein (Park & >>Miller and L'Ecuyer in particular). >> http://www.gnu.org/software/gsl/manual/gsl-ref_17.html > Just for completeness to the random generators mentioned above. > If your system has '/dev/random' and/or '/dev/urandom' then you have > also a good random to read from. This is feed by several non > deterministic data available on your system. The more usage and traffic > you have, the better. Those random generators have to be avoided, except in very specific cases as they are not reproducable; there is no way to replay them. Yannick -BEGIN PGP SIGNATURE- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Using GnuPG with Red Hat - http://enigmail.mozdev.org iD8DBQFDmJtoZY3s/IVpRFIRAhWVAKCZBuHVHPpzr5lHumXfBJcpDSidIQCfTlpn 72ZoHJeAXhK+ea58+TGQf4Y= =b3WV -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Random numbers generation
Hi All, On Thu, 2005-12-08 at 00:22, Stuart Prescott wrote: > Hi all, > > > /* create a generator chosen by the environment variable GSL_RNG_TYPE */ > > At the risk of straying further off topic, I can't help reminding > everyone of the importance of selecting a good random number generator > for scientific work (e.g. Monte Carlo simulations). There are far too > many crappy random number generators Out There and many of them are > still in widespread use. > > The GSL documentation talks a bit about the different generators > available and I highly recommend some of the references therein (Park & > Miller and L'Ecuyer in particular). > > http://www.gnu.org/software/gsl/manual/gsl-ref_17.html > > Personally, I have made use of the Marsaglia Random Number CD (once the > 10MB random bit files are loaded into memory in the disk cache, it's > quite fast) as a good source of reproducible pseudo-random numbers. > > http://stat.fsu.edu/pub/diehard/ > > or mirrored at (the CD seems to be missing from the original): > > http://www.cs.hku.hk/~diehard/cdrom/ > > The only disadvantage that I found was a little latency in starting > simulations in a cluster environment as the amount of data to be copied > to the computational node was greater. > Just for completeness to the random generators mentioned above. If your system has '/dev/random' and/or '/dev/urandom' then you have also a good random to read from. This is feed by several non deterministic data available on your system. The more usage and traffic you have, the better. Kind Regards, Thomas -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: [pkg-bioc] Re: Genetics Program
On 8 December 2005 at 18:03, Andreas Tille wrote: | Are you looking for biological software in and outside Debian in general? | I hope you noticed | | http://www.debian.org/devel/debian-med/microbio Nice page(s that I was in fact unaware of. I only need to know your med-* meta packages :) Dirk -- Statistics: The (futile) attempt to offer certainty about uncertainty. -- Roger Koenker, 'Dictionary of Received Ideas of Statistics' -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Packaging and Maintaining
Chris, On 8 December 2005 at 10:40, Christopher David Desjardins wrote: | Hi- | I am just starting to learn how to create and maintain debian packages. | I would like to help in package up some of these programs that we've | been discussing that might need some one to package them. I would be | especially interesting in package genetics software, QGIS, or R. Any | suggestions for packages that need to be maintained in particular would | be a great starting spot for me and would give me something to practice | on. The pkg-bioc project on Alioth would be a starting point. Packaging CRAN and BioC is easy and standardised, hence our aim of fully automating it. If you know Perl, you could dive right in, but it may help to download some R / CRAN packages first to see the structure, try debianising a local package or two and then play with the script. You need to get yourself an alioth id so that I can add you to the project. Andreas' URL to the Debian Med project also had a lot of bio/generics pointers. Hope this helps, Dirk -- Statistics: The (futile) attempt to offer certainty about uncertainty. -- Roger Koenker, 'Dictionary of Received Ideas of Statistics' -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Genetics Program
On 8 December 2005 at 18:09, Steffen Moeller wrote: | > What is the story with emboss? Couldn't find it for the currently ongoing | > preparations of the next Quantian update. Are there binaries somewhere? | EMBOSS would be lovely to have, indeed. Go and package it, I'm sure Andreas will sponsor it for you :) | > That is exactly the rub: I am not a BioC user, and I can't be the default | > maintainer for another few dozen (or dozen squared) packages. | Could we arrange a BioC repository for Alioth? Well we *do* have one in pkg-bioc [ which has refocussed on pkg-"CRAN and BioC" but not been renamed ]. | > Yes, and hopefully one day we'll be able to lean on someone with the need | > and the know to coordinate that. | | It would help in my understanding if not every maintainer of a package would | be required to become a full DD for the submission of updates. The acceptance | as a DD is quite a hurdle. Just as you "can't be partially pregnant", you can't have packages "partially inside Debian". If you are serious about contributing, join so that you can upload your packages so that they become fully-fledged packages, get autobuilt, ported, get BTS coverage etc pp Sponsoring, IMHO, doesn't scale to more than a few packages. I'd be happy to be proven wrong, but as our recent email exchange showed, I may have different expectations about QA for Debian packages than you :) Seriously, the tediousness of becoming a DD is known but please just stick it out. We could use your help. | I have never thought of it, but for BioC it should be possible to have such | events sponsored by some pharma directly, be it as Extremadura or elsewhe(re| | n). Maybe this would be a question for the BioC mailing list, I'll crosscheck | with the people I know. I'd be more interested if the focus was on both CRAN and BioC. Pharma money may come with strings attached. That said, let us know what you find out. The more the merrier. But we *do* have a standing offer to host Debian workshops in Spain. Why don't we go for it? Dirk -- Statistics: The (futile) attempt to offer certainty about uncertainty. -- Roger Koenker, 'Dictionary of Received Ideas of Statistics' -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Packaging and Maintaining
Hi- I am just starting to learn how to create and maintain debian packages. I would like to help in package up some of these programs that we've been discussing that might need some one to package them. I would be especially interesting in package genetics software, QGIS, or R. Any suggestions for packages that need to be maintained in particular would be a great starting spot for me and would give me something to practice on. Thanks, Chris -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Genetics Program
Hi all, Am Donnerstag 08 Dezember 2005 17:34 schrieb Dirk Eddelbuettel: > On 8 December 2005 at 16:55, Andreas Tille wrote: > What is the story with emboss? Couldn't find it for the currently ongoing > preparations of the next Quantian update. Are there binaries somewhere? EMBOSS would be lovely to have, indeed. > | > [ It is also unclear, at least to me, whether adding some 120 (for > | > BioC) packages (or 600-some in the case of CRAN) to Debian en bloc is > | > wise. ] But I want the apt-get'ability of CRAN and BioC, maybe from > | > outside archives. > | > | If you and probably other people as well who are interested in biological > | research I see no reason to keep these packages outside the official > | Debian > > That is exactly the rub: I am not a BioC user, and I can't be the default > maintainer for another few dozen (or dozen squared) packages. Could we arrange a BioC repository for Alioth? > | archive. I know that Debian-Med has at least one effect: We are winning > | users in the field of biology and medicine and we are winning them > | because we are at least promising to care for them - even if we proceed > | slowly. > > Yes, and hopefully one day we'll be able to lean on someone with the need > and the know to coordinate that. It would help in my understanding if not every maintainer of a package would be required to become a full DD for the submission of updates. The acceptance as a DD is quite a hurdle. > | > Now, to make this a tad more actionable: Would someone want to make > | > revival of this an item for the suggested Estremedura workshops and get > | > some people in the same room for two or three days to push this > | > further? Anybody care to run with that idea and organise it? > | > | Extremadura workshop about R? I guess this is a great idea! Even if I > | will not take part in one of the first announced meetings I hope to be > | there in at least one at the end of the year. > > Yes, it would be excellent to get a few interested people together to work > on this. I have never thought of it, but for BioC it should be possible to have such events sponsored by some pharma directly, be it as Extremadura or elsewhe(re| n). Maybe this would be a question for the BioC mailing list, I'll crosscheck with the people I know. Steffen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Genetics Program
On Thu, 8 Dec 2005, Dirk Eddelbuettel wrote: What is the story with emboss? Couldn't find it for the currently ongoing preparations of the next Quantian update. Are there binaries somewhere? Are you looking for biological software in and outside Debian in general? I hope you noticed http://www.debian.org/devel/debian-med/microbio There is a link to inofficial packages of Emboss, but the site of Matt Hope was reorganized. Find the sources of the package directly at http://debian.bioinformatics.unsw.edu.au/dists/sid/main/source/science/ The packages are for version 2.8 the latest upstream version seems to be 3.0. I started an Alioth project at http://alioth.debian.org/projects/pkg-emboss/ but this does not have any content yet. That is exactly the rub: I am not a BioC user, and I can't be the default maintainer for another few dozen (or dozen squared) packages. ACK. Kind regards Andreas. -- Wenn durch das Land die Grippe saust, es meiner ganzen Sippe graust. http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Genetics Program
On 8 December 2005 at 16:55, Andreas Tille wrote: | On Thu, 8 Dec 2005, Dirk Eddelbuettel wrote: | | > That ITP is officially dead. Action, if any, can be had around the pkg-bioc | > project on alioth where we have some rough code to spew out hundreds of .deb | > packages based on sources from both CRAN and BioC. | | I just notice that I was actually talking about the Emboss suite | (http://www.emboss.org/) and not bioconductor - but the situation seems | to be similar (if not worse than bioconductor). What is the story with emboss? Couldn't find it for the currently ongoing preparations of the next Quantian update. Are there binaries somewhere? | > [ It is also unclear, at least to me, whether adding some 120 (for | > BioC) packages (or 600-some in the case of CRAN) to Debian en bloc is wise. ] | > But I want the apt-get'ability of CRAN and BioC, maybe from outside archives. | | If you and probably other people as well who are interested in biological | research I see no reason to keep these packages outside the official Debian That is exactly the rub: I am not a BioC user, and I can't be the default maintainer for another few dozen (or dozen squared) packages. | archive. I know that Debian-Med has at least one effect: We are winning | users in the field of biology and medicine and we are winning them because | we are at least promising to care for them - even if we proceed slowly. Yes, and hopefully one day we'll be able to lean on someone with the need and the know to coordinate that. | > Now, to make this a tad more actionable: Would someone want to make revival | > of this an item for the suggested Estremedura workshops and get some people | > in the same room for two or three days to push this further? Anybody care to | > run with that idea and organise it? | | Extremadura workshop about R? I guess this is a great idea! Even if I | will not take part in one of the first announced meetings I hope to be | there in at least one at the end of the year. Yes, it would be excellent to get a few interested people together to work on this. Cheers, Dirk -- Statistics: The (futile) attempt to offer certainty about uncertainty. -- Roger Koenker, 'Dictionary of Received Ideas of Statistics' -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Genetics Program
On Thu, 8 Dec 2005, Dirk Eddelbuettel wrote: That ITP is officially dead. Action, if any, can be had around the pkg-bioc project on alioth where we have some rough code to spew out hundreds of .deb packages based on sources from both CRAN and BioC. I just notice that I was actually talking about the Emboss suite (http://www.emboss.org/) and not bioconductor - but the situation seems to be similar (if not worse than bioconductor). Welcome to the club, but, as you know, whining alone doesn't get us there either. Surely not. I just wanted to know if your local harddisk has perhaps better code than public archives and we could get some help from your site. [ It is also unclear, at least to me, whether adding some 120 (for BioC) packages (or 600-some in the case of CRAN) to Debian en bloc is wise. ] But I want the apt-get'ability of CRAN and BioC, maybe from outside archives. If you and probably other people as well who are interested in biological research I see no reason to keep these packages outside the official Debian archive. I know that Debian-Med has at least one effect: We are winning users in the field of biology and medicine and we are winning them because we are at least promising to care for them - even if we proceed slowly. One day someone with both an itch to scratch _and_ the will and time to work on it will push this further. Steffen Moeller did the last iteration and created a large number of apt-get'able packages. But that site was a one-off, hence has not been updated, was never fully checked against Policy, Lintian et al and may also have gotten temporarily lost in his move from Rostock to Luebeck. Steffen can tell you more. Well since Steffen moved he seems to be a little bit more busy than before. Perhaps he has to do some sightseeing in Lübeck first. ;-) Now, to make this a tad more actionable: Would someone want to make revival of this an item for the suggested Estremedura workshops and get some people in the same room for two or three days to push this further? Anybody care to run with that idea and organise it? Extremadura workshop about R? I guess this is a great idea! Even if I will not take part in one of the first announced meetings I hope to be there in at least one at the end of the year. Kind regards Andreas. -- Wenn durch das Land die Grippe saust, es meiner ganzen Sippe graust. http://fam-tille.de
Re: Genetics Program
On 8 December 2005 at 07:16, Andreas Tille wrote: | On Wed, 7 Dec 2005, Dirk Eddelbuettel wrote: | | > The next Quantian release will have once again a large selection of tools | > incl a complete set of BioConductor packages (that part is not in Debian) but | | What BioConductor version are you using? The BioConductor movement to Naturally the current BioConductor release 1.7. | official Debian is a little bit stalled. Matt Hope has an ITP, inofficial | packages of an old version and no time to respond to any question. I would That ITP is officially dead. Action, if any, can be had around the pkg-bioc project on alioth where we have some rough code to spew out hundreds of .deb packages based on sources from both CRAN and BioC. | love if we could get this beast into Debian but have no time to care | for it personally. Other people who claimed to have interest and wanted to | do work on an alioth project I have started seemed to have lost interest. Welcome to the club, but, as you know, whining alone doesn't get us there either. [ It is also unclear, at least to me, whether adding some 120 (for BioC) packages (or 600-some in the case of CRAN) to Debian en bloc is wise. ] But I want the apt-get'ability of CRAN and BioC, maybe from outside archives. One day someone with both an itch to scratch _and_ the will and time to work on it will push this further. Steffen Moeller did the last iteration and created a large number of apt-get'able packages. But that site was a one-off, hence has not been updated, was never fully checked against Policy, Lintian et al and may also have gotten temporarily lost in his move from Rostock to Luebeck. Steffen can tell you more. Now, to make this a tad more actionable: Would someone want to make revival of this an item for the suggested Estremedura workshops and get some people in the same room for two or three days to push this further? Anybody care to run with that idea and organise it? Regards, Dirk -- Statistics: The (futile) attempt to offer certainty about uncertainty. -- Roger Koenker, 'Dictionary of Received Ideas of Statistics' -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
