From biopython-bugs at bioperl.org Fri Mar 1 00:15:43 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Notification: incoming/61 Message-ID: <200203010515.g215FhkO030820@pw600a.bioperl.org> JitterBug notification new message incoming/61 Message summary for PR#61 From: katel@worldpath.net Subject: interface Date: Fri, 1 Mar 2002 00:15:42 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From katel@worldpath.net Fri Mar 1 00:15:42 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g215FgkO030816 for ; Fri, 1 Mar 2002 00:15:42 -0500 Date: Fri, 1 Mar 2002 00:15:42 -0500 Message-Id: <200203010515.g215FgkO030816@pw600a.bioperl.org> From: katel@worldpath.net To: biopython-bugs@bioperl.org Subject: interface Full_Name: Katharine Lindner Module: ParserSupport Dispatch Version: development OS: Windows 98 Submission from: (NULL) (209.187.114.149) in _parse_elements, the consumer and its container, content handler, are confused. The code checks the attribute _content_handler to see if it is a subclass of Dispatch. But _content_handler._consumer is the attribute that should be checked. I tested this on a copy of ParserSupport. But this is not the solution because _consumer is a private variable. It needs an accessor. From chapmanb at arches.uga.edu Tue Mar 5 08:52:31 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Neural Networks In-Reply-To: References: Message-ID: <20020305085231.B91286@ci350185-a.athen1.ga.home.com> Hi Yair; Sorry for the delay in responding. Hackin' and fun in South Africa has been distracting my attention. > I see you added a new Neural Network module. Do you have some documentation > for it? I started writing some docs for it a while back, but never finished due to some problems with focusing my mind, I guess. The docs that are there should help you get started -- one day I'll hopefully finish the docs and get them into the Biopython tutorial. You can pick up the documentation I have from: http://bioinformatics.org/bradstuff/bp/PGML_Tutorial.pdf Hope this helps! Feel free to ask if you have problems. Brad From Y.Benita at pharm.uu.nl Tue Mar 5 09:03:46 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Neural Networks In-Reply-To: <20020305085231.B91286@ci350185-a.athen1.ga.home.com> Message-ID: on 5/3/2002 14:52, Brad Chapman at chapmanb@arches.uga.edu wrote: > I started writing some docs for it a while back, but never finished due > to some problems with focusing my mind, I guess. The docs that are there > should help you get started -- one day I'll hopefully finish the docs > and get them into the Biopython tutorial. > > You can pick up the documentation I have from: > > http://bioinformatics.org/bradstuff/bp/PGML_Tutorial.pdf Hi Brad, Thanks for the docs. I am already into NN testing different pacakages and stuff. I do have some python functions to generate input files for NN on the basis of sparse coding. Can this be interesting for you? Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From chapmanb at arches.uga.edu Tue Mar 5 09:11:54 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Neural Networks In-Reply-To: References: <20020305085231.B91286@ci350185-a.athen1.ga.home.com> Message-ID: <20020305091154.A7537@ci350185-a.athen1.ga.home.com> Hi Yair; > Thanks for the docs. I am already into NN testing different pacakages and > stuff. I do have some python functions to generate input files for NN on the > basis of sparse coding. Can this be interesting for you? Definately! I'm glad to hear you are interested in Neural Network stuff, I haven't had much time to work on it recently, so would be very happy to have someone else contributing to it. I'll admit that I don't know anything beyond the basics of sparse coding, but I'll be very happy to add code/docs/whatever into the Neural Network package if you have them. Glad you're interested in this! Brad From Y.Benita at pharm.uu.nl Tue Mar 5 09:39:42 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Neural Networks In-Reply-To: <20020305091154.A7537@ci350185-a.athen1.ga.home.com> Message-ID: on 5/3/2002 15:11, Brad Chapman at chapmanb@arches.uga.edu wrote: > I'll admit that I don't know anything beyond the basics of sparse > coding, but I'll be very happy to add code/docs/whatever into the Neural > Network package if you have them. OK, I will read your docs and try to understand what you did and I will organize my code to fit it. From chapmanb at arches.uga.edu Tue Mar 5 10:15:39 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Neural Networks In-Reply-To: References: <20020305091154.A7537@ci350185-a.athen1.ga.home.com> Message-ID: <20020305101539.B7537@ci350185-a.athen1.ga.home.com> > OK, I will read your docs and try to understand what you did and I will > organize my code to fit it. Sounds great -- let me know if things don't make sense, or you need help or whatever. > From my initial tests it looks like the NN is very slow with the huge amount > of data generated by sparse coding. I am not sure python is suitable for > this but we can always give it a try. Worst case scenario is to use it for > translating biological data to fit the input and translating the output back > to biological data. The actual calculation can then be done by a C based > engine. Yup, python is definitely not speedy for neural networks. The optimal solution would be to determine if the current framework I have makes sense and, if so, code up the slow parts in C. Alternatively you could hook into an existing NN engine, but I don't know much about what is available. I worked in python so I could learn Neural Network stuff, which is why I didn't choose to go this route. Let me know how things work out for you. Brad From katel at worldpath.net Wed Mar 6 21:30:35 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] user survey Message-ID: <003301c1c580$1561c7e0$08fea8c0@pcklindner> NCBI has a user survey on what the bioinformatics community needs. It is available at ncbi.nlm.nih.gov/About/proteinsurvey/ It could be useful in setting our priorities. Cayte From katel at worldpath.net Tue Mar 12 23:57:04 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] new parsers Message-ID: <003c01c1ca4b$8664de80$08fea8c0@pcklindner> I have a couple of new parsers ready to commit. Although the tests pass on my system, they will definitely break on the main system, because I patched Dispatch to fix a bug. Hopefully the official fix will be made when the dust settles from the hackathon. For now should I wait? Cayte From katel at worldpath.net Wed Mar 13 00:02:13 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] biocorba Message-ID: <004401c1ca4c$3e494900$08fea8c0@pcklindner> Recently I finished a book called Art of the Genes. The ideas in the book screamed out for computer simulation and I started writing python code. Its crude but hopefully this will be a start and others can jump in with more sophisticated ideas. I'd like to do the graphics in java, because python is pretty limited in this regard. ould biocorba be the best glue? Cayte From chapmanb at arches.uga.edu Wed Mar 13 11:07:09 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] biocorba In-Reply-To: <004401c1ca4c$3e494900$08fea8c0@pcklindner> References: <004401c1ca4c$3e494900$08fea8c0@pcklindner> Message-ID: <20020313110709.A5779@ci350185-a.athen1.ga.home.com> Hi Cayte; > Recently I finished a book called Art of the Genes. Mmmm, development. Don't know if I could bring myself to read this after all of those painful papers on fly wing development I sludged through in genetics :-). > I'd like to do the graphics in java, because python is > pretty limited in this regard. What kind of stuff do you want to do? There are quite a few libraries out there for python for tons of different things -- although, I hear the java 3D drawing code is very nice; I don't know if there is anything equivalent for python. Then again, I don't do much graphics stuff. Pretty pictures are not my forte; sadly my brother got all the art skills in the family. > could biocorba be the best glue? Not sure exactly what you are doing, but BioCorba is meant for trasferring sequence-style objects with features and annotations and the like. If you are doing stuff like this BioCorba works great -- the interoperability with the BioJava implementation had lots of testing at the hackathon, and appears to be mostly bug-free (fingers crossed :-). If you are doing fancier stuff, jython might be your best bet. Brad From chapmanb at arches.uga.edu Wed Mar 13 11:10:49 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] new parsers In-Reply-To: <003c01c1ca4b$8664de80$08fea8c0@pcklindner> References: <003c01c1ca4b$8664de80$08fea8c0@pcklindner> Message-ID: <20020313111049.B5779@ci350185-a.athen1.ga.home.com> Hey again Cayte; > I have a couple of new parsers ready to commit. Although the tests pass > on my system, they will definitely break on the main system, because I > patched Dispatch to fix a bug. Well, I have to admit I have no idea what Dispatch is, but if there is a bug you should definitely fix it. Whos code is this? -- maybe they can confirm it. > Hopefully the official fix will be made when > the dust settles from the hackathon. For now should I wait? Plenty o' dust has settled. The jet lag is mostly gone and it's back to the ol' grind of work. Sigh, no more Africa. Brad From katel at worldpath.net Mon Mar 18 23:25:53 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] blocks Message-ID: <004f01c1cefe$299db160$08fea8c0@pcklindner> Is anyone working on blocks now? If not, I'd like to write a parser. Cayte From d.navarro at bmb.sdu.dk Thu Mar 28 06:27:12 2002 From: d.navarro at bmb.sdu.dk (Danny Navarro) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] biopython in ZOPE volunteer Message-ID: <1017314832.1080.58.camel@boli> Hi all, I am a "curious" biochemistry/bioinformatics undergraduate student who always have liked very much computers and specially Open Source. Right now, I am able to write some code in Python and Perl, I have some skills administrating Debian servers,... and I know more "just for fun" computer things. But I don't know what can I do to be useful for the open bioinformatics community. I would like to help to make it stronger. One thing I am very enthusiastic about is the idea of wrapping biopython modules in ZOPE, so that you can construct web sites with ZOPE and at the same time provide bioinformatics web services using biopython modules. What it'll be really cool woud be the intercommunication between biopython and ZOPE APIs. To do this: would be better to extend ZOPE adding a "biopython product" using Zclasses? ...or would be better the implementation in the biopython API the accession to the ZOPE one? (like bioperl with MySQL) ... or both might be required? I have seen some recent messages in the mailing list archive regarding to this matter: http://www.biopython.org/pipermail/biopython-dev/2002-January/000802.html ================================================== > Biopython zope objects complete with interface (Blast, .....) and output > (BioXML,....) > Bioperl zope objects complete with interface (T-coffee) and output > (BioXML, GAME, ...) > Web maintainers could just install the products and Voila. > Biopython ZClasses (and maybe BioPerl objects?) could be subclassed for > special uses through properties interface. > The output of one zope product could be fed into another allowing for > complex scripts. > A weird example. > From Swissprot chose trypsin->fasta->phylogeny->align each > group->consesus for each group->common restriction enzymes, ..... I think these are the sort of ideas that need to be shared with the Biopython (and possibly Bioperl) developers! :-) =================================================== http://www.biopython.org/pipermail/biopython/2000-August/000350.html =================================================== And here's the kicker: - Existing Python modules can be imported into Zope's namespace and be exposed to the Web. With a little bit of wrapping, it may eventually be possible to build a set of reusable "web widgets" to wrap Biopython objects. This is still a very vaguely formed idea, but it is where I think I would like to work towards, eventually. It would mean that the site could actually contribute towards the Biopython project in a more concrete manner than just providing PR. Now firstly... do we have the go-ahead to start spending some time on this? Jeff? :-) ===================================================== Ok, so these kinds things I would really like to do. So if you want a quick learner volunteer to colaborate in this possible project just say me what I can do, please. Danny From dyoo at acoma.Stanford.EDU Thu Mar 28 14:45:07 2002 From: dyoo at acoma.Stanford.EDU (Danny Yoo) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] An equivalent to Bioperl's Bio::Seq::LargeSeq? Message-ID: Hi everyone, Has anyone been working on extending Seq.py extension to read large sequences? I didn't see anything like this in Biopython, and I'd be happy to work on this if anyone's interested. Here's the bits of code that I have so far: ###### ""IOString.py --- Make files look like Python strings. Danny Yoo (dyoo@acoma.stanford.edu) This module implements a class that presents a file as if it were a string sequence. This is meant to do the opposite of Python's StringIO. But why would anyone want to do something like this, instead of just doing a simple open(file).read()? Because some strings may be too huge to keep in memory at once, but we may still want to manipulate slices of it as if it were a string. """ class IOString: def __init__(self, file): """Initialize a new IOString from a given file. If 'file' is a string, assume the user is giving us a filename, and automatically open the file.""" if type(file) == type(""): file = open(file) self.file = file def __getitem__(self, i): """Return a single character at index i.""" if i < 0: i = len(self) + i if i >= len(self): raise IndexError, "IOString index out of range" self.file.seek(i) return self.file.read(1) def __getslice__(self, i, j): """Note: __getslice__() is deprecated as of Python 2.0. Perhaps it might be better to push this functionality in __getitem__() """ if i < 0: i = len(self) + i if j < 0: j = len(self) + j j = min(j, len(self)) if i > j: return '' self.file.seek(i) return self.file.read(j-i) def __repr__(self): return "IOString(%s)" % repr(self.file) """We'll only print out up to 100 characters.""" MAX_STR_DISPLAYED = 100 def __str__(self): self.file.seek(0) if len(self) < self.MAX_STR_DISPLAYED: return self[:] else: return self[:self.MAX_STR_DISPLAYED] + " [...]" def __len__(self): self.file.seek(0, 2) ## Seek to the end return int(self.file.tell()) ###### This code tries to provides a nice read-only string interface for files on disk: ### >>> import IOString >>> s = IOString.IOString("/home/arabidopsis/bacs/CHR1/F10A5.xml") >>> print s >> s[-50:] 'TGGAATTC\n\t\n\n' >>> len(s) 318459 ### At the moment it doesn't support any of the other string methods, nor does it yet allow people to search through it with a regular expression without turning the whole thing back into a string. However, when I have time, I can try to make a C extension similar to IOString.py that implements the read-only buffer interface so that this works nicely with regular expressions. From katel at worldpath.net Thu Mar 28 19:46:27 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Last chance to claim Dispatch bug fix Message-ID: <002e01c1d6bb$2a40c200$08fea8c0@pcklindner> Unless Andrew or Jeff objects I plan to add an accessor to _consumer in ParserSupport and change Parser in Martel to check for Dispatch through the accessor. I need it because I've accumulated three new format parsers that depend on Dispatch. I'd like to check them in. Cayte From jchang at smi.stanford.edu Fri Mar 29 00:03:41 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Last chance to claim Dispatch bug fix In-Reply-To: <002e01c1d6bb$2a40c200$08fea8c0@pcklindner> References: <002e01c1d6bb$2a40c200$08fea8c0@pcklindner> Message-ID: <20020328210341.E440@krusty.stanford.edu> Hi Cayte, Could you please describe your fixes in a little more detail? For example, I'm not sure what you're planning on doing with _consumer in ParserSupport, or what problem it's trying to solve. Also, for _consumer, are you referring to the member variable of the EventGenerator or SGMLStrippingConsumer, or something else? Jeff On Thu, Mar 28, 2002 at 04:46:27PM -0800, Cayte wrote: > Unless Andrew or Jeff objects I plan to add an accessor to _consumer in > ParserSupport and change Parser in Martel to check for Dispatch through the > accessor. I need it because I've accumulated three new format parsers that > depend on Dispatch. I'd like to check them in. > > Cayte > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From d.navarro at bmb.sdu.dk Fri Mar 29 09:41:07 2002 From: d.navarro at bmb.sdu.dk (Danny Navarro) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] biopython in ZOPE volunteer In-Reply-To: <20020328114448.22141.qmail@web10806.mail.yahoo.com> References: <20020328114448.22141.qmail@web10806.mail.yahoo.com> Message-ID: <1017412868.2789.78.camel@boli> Hi Florian, My first mail was some rough ideas. I was trying to get some collaboration to do it. I still have to maturate more the ideas. But even if I don't find collaboration in the beginning I'll be sending my progress. Right now, I am reading lots of docs about biopython and Zope in order to come out soon with a clear idea about how to integrate them. My guess now is that I'll use Zclasses to wrap biopython to do it. But I want to evaluate more possibilities. Wishes. On Thu, 2002-03-28 at 12:44, Florian Graefe wrote: > Dear Danny. > > i am interested in your ideas ( even if they are obvious ). > > So, send me an email explaining what you are thinking you can do. > > > Best wishes > > Florian > > --- Danny Navarro wrote: > > Hi all, > > > > I am a "curious" biochemistry/bioinformatics undergraduate student who > > always have liked very much computers and specially Open Source. > > > > Right now, I am able to write some code in Python and Perl, I have some > > skills administrating Debian servers,... and I know more "just for fun" > > computer things. > > > > But I don't know what can I do to be useful for the open bioinformatics > > community. I would like to help to make it stronger. > > > > One thing I am very enthusiastic about is the idea of wrapping biopython > > modules in ZOPE, so that you can construct web sites with ZOPE and at > > the same time provide bioinformatics web services using biopython > > modules. > > > > What it'll be really cool woud be the intercommunication between > > biopython and ZOPE APIs. To do this: > > > > would be better to extend ZOPE adding a "biopython product" using > > Zclasses? > > > > ...or would be better the implementation in the biopython API the > > accession to the ZOPE one? (like bioperl with MySQL) > > > > ... or both might be required? > > > > I have seen some recent messages in the mailing list archive regarding > > to this matter: > > > > http://www.biopython.org/pipermail/biopython-dev/2002-January/000802.html > > > > ================================================== > > > Biopython zope objects complete with interface (Blast, .....) and > > output > > > (BioXML,....) > > > Bioperl zope objects complete with interface (T-coffee) and output > > > (BioXML, GAME, ...) > > > Web maintainers could just install the products and Voila. > > > Biopython ZClasses (and maybe BioPerl objects?) could be > > subclassed for > > > special uses through properties interface. > > > The output of one zope product could be fed into another allowing > > for > > > complex scripts. > > > A weird example. > > > From Swissprot chose trypsin->fasta->phylogeny->align each > > > group->consesus for each group->common restriction enzymes, ..... > > > > I think these are the sort of ideas that need to be shared with the > > Biopython (and possibly Bioperl) developers! :-) > > =================================================== > > > > http://www.biopython.org/pipermail/biopython/2000-August/000350.html > > > > =================================================== > > And here's the kicker: > > > > - Existing Python modules can be imported into Zope's namespace and > > be > > exposed to the Web. With a little bit of wrapping, it may > > eventually be > > possible to build a set of reusable "web widgets" to wrap > > Biopython > > objects. This is still a very vaguely formed idea, but it is > > where I think > > I would like to work towards, eventually. It would mean that the > > site > > could actually contribute towards the Biopython project in a more > > concrete > > manner than just providing PR. > > > > Now firstly... do we have the go-ahead to start spending some time > > on this? > > Jeff? :-) > > ===================================================== > > > > Ok, so these kinds things I would really like to do. > > > > So if you want a quick learner volunteer to colaborate in this possible > > project just say me what I can do, please. > > > > Danny > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > > __________________________________________________ > Do You Yahoo!? > Yahoo! Movies - coverage of the 74th Academy Awards? > http://movies.yahoo.com/ From katel at worldpath.net Fri Mar 29 18:39:48 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Last chance to claim Dispatch bug fix References: <002e01c1d6bb$2a40c200$08fea8c0@pcklindner> <20020328210341.E440@krusty.stanford.edu> Message-ID: <001d01c1d77b$07cfe960$08fea8c0@pcklindner> ----- Original Message ----- From: "Jeffrey Chang" To: "Cayte" Cc: Sent: Thursday, March 28, 2002 9:03 PM Subject: Re: [Biopython-dev] Last chance to claim Dispatch bug fix > Hi Cayte, > > Could you please describe your fixes in a little more detail? For > example, I'm not sure what you're planning on doing with _consumer in > ParserSupport, or what problem it's trying to solve. Also, for > _consumer, are you referring to the member variable of the > EventGenerator or SGMLStrippingConsumer, or something else? > > Jeff > Yes I'm referring to the member variable of EventGenerator. _parse_elements in Parser in Martel contains a test where it checks the content handler to see if it is a subclass of Dispatch. The test does not work as intended because Event Generator is a decorator not a subclass of Dispatch. So I need to dive in and check if EventGenerator._consumer is a subclass of Dispatch. Its cheating to look up underscored variables. An accessor would be better. The fix works fine on my hacked up version at home. But if I check in my new parsers without the fix someone will run the unit tests on the CVS code and ask why it doesn't work. Cayte From adalke at mindspring.com Sat Mar 30 00:12:41 2002 From: adalke at mindspring.com (Andrew Dalke) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Fw: Risks Digest 21.98 Message-ID: <022201c1d842$e1b41080$8dccf7a5@josiah> This comes from the most recent RISKS article. >***** See last item for further information, disclaimers, caveats, etc. ***** >This issue is archived at >and by anonymous ftp at ftp.sri.com, cd risks . > ... >Date: Wed, 13 Mar 2002 18:26:28 +1300 >From: "Dr Richard A. O'Keefe" >Subject: Bioinformatics start-of-the-art > >Bioinformatics is a hot topic at this university, and the computer science >department is just starting to get involved. As part of trying to learn >about this field, I thought I'd read a couple of the better-known programs. >To be honest, I thought I'd run splint (formerly known as lclint) over them >and find a minor buig or two. I'm not going to name either of these >programs, but one of them was particularly interesting because we were >thinking of having a student make a parallel version to try out a parallel >architecture one of our people is interested in, because normal runs of this >program on recent PCs can take about 3 weeks. > >I don't know what art these programs are state-of; possibly macrame. >They certainly aren't even 1970's state of the programming art. > >* indentation inconsistent, crazy, or both (fix with indent) - lines up > to 147 columns wide (fix with indent) >* lots of dead variables (fix with quick edit) >* array subscripts that could go negative (use unsigned char rather than > char in a couple of dozen places, phew) >* failure to comprehend that C++ prototypes and C prototypes are > different (fix by changing () to (void) in too many places) >* #define lint ... so that lint falls over (rename lint to Lint in a > dozen files) >* assumption that long int = 32 bits (one program) or that int = 32 bits > (the other) (not yet done, but use inttypes.h with a local backup) >* string->integer code that gets INT_MIN wrong (rip out, plug in code > known since 60s) >* using %ld format with int arguments (*printf and *scanf), a real > problem because the machines > (I have access to are 64-bitters and it'd be nice if the programs ran > in LP64 mode.) >* gcc, liint, splint find variable used before initialised (see next > item) >* technically legal syntax with no semantics: double matrix[][] as > function argument,. (Scream, bang head on wall, write this message.) > >Is it reasonable to expect people with a biochemistry or mathematics >background to write clean well-engineered code? No. For the importance of >the topic, and the sums of money involved, is it reasonable to expect that >they'll have their programs cleaned by someone else before release? I think >it is. With the pervasive lack of quality I'm seeing, I don't trust _any_ >of the results of these programs. I have to wonder how many published >results obtained using these programs (and fed back into databases that are >used to derive more results which are ...) are actually valid. Andrew dalke@dalkescientific.com