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Home=20 Page|| Sitemap=20 || A-Z Directory ||= OASIS=20 Online=20 || In Detail ||=20 Calendar of Eve= nts || Expat=20 Links || Consulates=20 || Emergency=20 Contact Numbers || Clubs=20 & Associations || Restaurants=20 || Bars<= /A>=20 || Nightclubs||=20 Real=20 Estate || Classif= ieds ||=20 Shopping=20 || Art=20 ||<= /SMALL>=20 Theatre=20 ||=20 MESSAGE TRUNCATED AT 8192 <==== From Y.Benita at pharm.uu.nl Mon May 13 02:09:32 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:12 2005 Subject: [BioPython] Re: [Biopython-dev] EuroPython: call for speaker In-Reply-To: Message-ID: Hi all, I am not really participating in the development of biopython. Basically I am a User and I manage to maintain an updated Mac version. That said I can tell you I live in the Netherlands, 2 hours driving distance from Belgium. If you are very desperate and can't find a speaker maybe you can tell me what needs to be done and I will let you know if I am up to it. Yair -- Yair Benita Pharmaceutical Proteomics Faculty of Pharmacy The Netherlands on 2/5/02 17:23, Iddo Friedberg at idoerg@cc.huji.ac.il wrote: > Hi Nicolas, Brad and all! > > Synopsis: looking for a European biopython person to present the project > at the EuroPython conference http://www.europython.org/ > > So sorry, but I won't be able to make it. I'm running a tight schedule > here trying to finish my PhD, so conferences are pretty much out for me > right now (including BOSC, boo-hoo!). I crossposted this to the regular > biopython list, which has a wider audience. C'mon folks, Belgium is lovely > in June (or any other time of the year, for that matter). > > Iddo > > > > On Thu, 2 May 2002, Nicolas Chauvat wrote: > > : > I'm not at all European, but I do live on the east coast of the US, so > : > if there were some travel-monies available I'd be more than happy to > : > travel to Europe :-). > ? > : Well, that's the thing: it's kind of a volunteer-organized conference, and > : we're not sure yet we'll have that much money to fly people over... > ? > : > Seriously, I can think of at least a couple Europe-close people, Iddo > : > (although, he may have moved to California, can't remember when that > : > was happening) and Thomas (mmmm, Copenhagen). Either of you > : > interested? Anyone else 'round that I've forgotten? > ? > : I asked thomas already, but he will be on vacation at that time. > ? > : Iddo: please let me know if you're interested and how far you live from > : Belgium. > ? > : > Once-biopython-gets-Europe-we-begin-the-conquest-of-the-world-ly yr's, > ? > : I also got in touch with Laurent Pierron, from LORIA (fr), that offered to > : present BioPython. I'll let the list know how it ends. > ? > : Cheers ! > ? > ???? > : Nicolas Chauvat From Y.Benita at pharm.uu.nl Mon May 13 12:06:28 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Presentation of biopython Message-ID: Hi all, I volunteered to give a short talk about biopython in the EuroPython conference. I am sure some of you have done it before. I will appreciate useful suggestions, slides, notes or thoughts. Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From katel at worldpath.net Mon May 13 17:34:05 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Finally! Subclass of Dispatch working Message-ID: <002501c1fac5$e98392e0$08fea8c0@pcklindner> A subclass of Dispatch works now! Jeff suggested double inheritance from EventGenerator and Dispatch. EventGenerator has the glue to the Martel tags. Dispatch has a better callback mechanism that allows calls to nested tags. goose = Group( "goose", Str( "goose" ) ) gaggle = Group( "gaggle", RepN( goose ) ) With Dispatch you can call back on both goose and gaggle without conflict. I thought multiple inheritance would be a mess but it turns out all I have to add is one member variable, interest_tags to the Dispatch subclass. I suggest adding it to Dispatch itself tp prevent confusion. Hopefully I can submit some parsers that were on hold after I check the output. Cayte From katel at worldpath.net Wed May 15 00:48:20 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Saf parser commited Message-ID: <001801c1fbcb$c3639220$08fea8c0@pcklindner> The newly commited Saf parser works on my Win98 system. If others wish to test it on Linux it may prevent wild goose chases later. I also have a GEO parser but I'd like to check it more closely before I add it to CVS. Cayte From katel at worldpath.net Fri May 17 02:06:39 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] bots and spiders Message-ID: <002001c1fd69$03987100$08fea8c0@pcklindner> Looking at some of the proteomics databases like CDD and SMART, the information is spread over more than one web page Eventually we may need bots to parse information from multiple pages. It could either parse on the fly or collect pages and then parse. Cayte From Y.Benita at pharm.uu.nl Thu May 23 07:21:26 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] New module for analysis of DNA and Protein sequences Message-ID: Hi all, I am doing some DNA and protein analysis and I have arranged all my scripts in one module. It contains two classes: DnaAnalysis and ProteinAnalysis. Both classes use a sequence object as input (from Seq.py). DnaAnalysis: calculates nucleotide content, GC content,codon adaptation index, translation to protein (with Tools.translate) and gives access to the ProteinAnalysis class. ProteinAnalysis: calculates amino acid content, molecular weight, protein stability, flexibility, hydrophobicity, pi. I also have a module for calculating the area under the curve. It is useful, for instance, to know which fraction of a protein is hydrophobic and which is hydrophilic. It is more informative than averaging. I am not sure if I should include this. Let me know what to do next. I am not sure how it works for submitting modules and what is the procedure. Is someone checking the code? Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From jchang at smi.stanford.edu Fri May 24 05:10:45 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] New module for analysis of DNA and Protein sequences In-Reply-To: ; from Y.Benita@pharm.uu.nl on Thu, May 23, 2002 at 01:21:26PM +0200 References: Message-ID: <20020524021044.E9652@springfield.stanford.edu> Are some of these functions duplicates of existing biopython functionality? I believe Thomas has already implemented some of this stuff in sequtils.py, so please work with him on figuring out how to integrate things. I want to avoid duplicate code. Also, be sure that you are willing to license it with the Biopython license, are willing to maintain it, and are the copyright holder and have the legal right to submit the code under these terms. Jeff On Thu, May 23, 2002 at 01:21:26PM +0200, Yair Benita wrote: > Hi all, > I am doing some DNA and protein analysis and I have arranged all my scripts > in one module. It contains two classes: DnaAnalysis and ProteinAnalysis. > Both classes use a sequence object as input (from Seq.py). > > DnaAnalysis: calculates nucleotide content, GC content,codon adaptation > index, translation to protein (with Tools.translate) and gives access to the > ProteinAnalysis class. > > ProteinAnalysis: calculates amino acid content, molecular weight, protein > stability, flexibility, hydrophobicity, pi. > > I also have a module for calculating the area under the curve. It is useful, > for instance, to know which fraction of a protein is hydrophobic and which > is hydrophilic. It is more informative than averaging. I am not sure if I > should include this. > > Let me know what to do next. I am not sure how it works for submitting > modules and what is the procedure. Is someone checking the code? > > Yair > -- > Yair Benita > Pharmaceutical Proteomics > Utrecht University > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From Y.Benita at pharm.uu.nl Fri May 24 05:44:52 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] New module for analysis of DNA and Protein sequences In-Reply-To: <20020524021044.E9652@springfield.stanford.edu> Message-ID: I see that some are duplicates. I was not aware of these functions. Thomas wrote it for PCR related issues. I have other things in mind. Maybe I can fix it to use the code of Thomas for the duplicated functions. I also think we should seriously consider revising the documentation of biopython. Many things have changed and if someone wants to know what kind of methods are available in biopython he has to go though the code and read the comments. Regarding legal issues, I do not see any problems. Is there a web page with instructions or guidelines? I could not find anything on the biopython web site. Yair on 24/5/02 11:10, Jeffrey Chang at jchang@smi.stanford.edu wrote: > Are some of these functions duplicates of existing biopython > functionality? I believe Thomas has already implemented some of this > stuff in sequtils.py, so please work with him on figuring out how to > integrate things. I want to avoid duplicate code. > > Also, be sure that you are willing to license it with the Biopython > license, are willing to maintain it, and are the copyright holder and > have the legal right to submit the code under these terms. > > Jeff > > > On Thu, May 23, 2002 at 01:21:26PM +0200, Yair Benita wrote: >> Hi all, >> I am doing some DNA and protein analysis and I have arranged all my scripts >> in one module. It contains two classes: DnaAnalysis and ProteinAnalysis. >> Both classes use a sequence object as input (from Seq.py). >> >> DnaAnalysis: calculates nucleotide content, GC content,codon adaptation >> index, translation to protein (with Tools.translate) and gives access to the >> ProteinAnalysis class. >> >> ProteinAnalysis: calculates amino acid content, molecular weight, protein >> stability, flexibility, hydrophobicity, pi. >> >> I also have a module for calculating the area under the curve. It is useful, >> for instance, to know which fraction of a protein is hydrophobic and which >> is hydrophilic. It is more informative than averaging. I am not sure if I >> should include this. >> >> Let me know what to do next. I am not sure how it works for submitting >> modules and what is the procedure. Is someone checking the code? >> >> Yair >> -- >> Yair Benita >> Pharmaceutical Proteomics >> Utrecht University >> >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > From Y.Benita at pharm.uu.nl Fri May 24 06:07:52 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] PCR module Message-ID: Thomas, I have looked at your sequtils module and I can add some code from my own PCR module: Melting temperature of primers. Matching primers to a template, including primers with overhangs. Checking the frame of the product vs the template (only for primers which contain a gateway adapter, otherwise I cannot know the frame of the primer). I plan to add some primer selection code but I first have to analyze 1600 PCR reactions we did and improve the primer selection based on that. Would you like to see the code and add it to your module or would you prefer that I write a module that uses sequtils and adds new methods? Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From thomas at cbs.dtu.dk Fri May 24 06:23:10 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: References: Message-ID: Yair Benita writes: > Thomas, > I have looked at your sequtils module and I can add some code from my own > PCR module: > > Melting temperature of primers. > Matching primers to a template, including primers with overhangs. > Checking the frame of the product vs the template (only for primers which > contain a gateway adapter, otherwise I cannot know the frame of the primer). > > I plan to add some primer selection code but I first have to analyze 1600 > PCR reactions we did and improve the primer selection based on that. > > Would you like to see the code and add it to your module or would you prefer > that I write a module that uses sequtils and adds new methods? > I am still moving from the danish university to the swedish university, so I was not involved in any biopython discussions for a time ... Anyway, the purpose of sequtils was more like a temporary storage module for commonly used sequence analyzing utilities/functions. I hoped that most of the functions would eventually find their way into the modules they actually should belong too .... Whats the overall opinion of sequtils.py? * Should we reorganize the code and move "movable" functions before merging/adding PCR modules and documentation? * Should we use it as it is (maybe after some cosmetic changes) and continue adding sequence analyzing methods? * Or, should we split it into core sequence utilities (like GC content and sequence editing) and more user level defined sequence utilities (like 6 frame translations, gc skews, graphical GC content etc.) (inherited from the core module) Personally, I'd prefer the latter ... in this case we could have a PCR module and avoiding duplicated code by putting common functions in the core sequence utilities module (e.g. GC content, frames etc.) Suggestions, ideas, critics??? its-hot-even-here-in-sweden'ly y'rs -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas@biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From jchang at smi.stanford.edu Fri May 24 16:29:21 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] New module for analysis of DNA and Protein sequences In-Reply-To: ; from Y.Benita@pharm.uu.nl on Fri, May 24, 2002 at 11:44:52AM +0200 References: <20020524021044.E9652@springfield.stanford.edu> Message-ID: <20020524132919.A22712@springfield.stanford.edu> On Fri, May 24, 2002 at 11:44:52AM +0200, Yair Benita wrote: > I also think we should seriously consider revising the documentation of > biopython. Many things have changed and if someone wants to know what kind > of methods are available in biopython he has to go though the code and read > the comments. I agree. However, maintaining current docs for these projects are hard. Everybody's pretty busy... > Regarding legal issues, I do not see any problems. > Is there a web page with instructions or guidelines? I could not find > anything on the biopython web site. The FAQ needs to be updated too! ;) Jeff From Y.Benita at pharm.uu.nl Sat May 25 04:22:38 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] New module for analysis of DNA and Protein sequences In-Reply-To: <20020524132919.A22712@springfield.stanford.edu> Message-ID: Eveybody's always busy. The trick is to split the load between us, not only those who maintain a module have to write the docs, others can help and it will be verified later. Writing code that no one knows exist is a waist of time. Furthermore, documenting should be a continuous process just like developing. The longer we wait now the harder it will be to write it. Yair on 24/5/2002 22:29, Jeffrey Chang at jchang@smi.stanford.edu wrote: > On Fri, May 24, 2002 at 11:44:52AM +0200, Yair Benita wrote: >> I also think we should seriously consider revising the documentation of >> biopython. Many things have changed and if someone wants to know what kind >> of methods are available in biopython he has to go though the code and read >> the comments. > > I agree. However, maintaining current docs for these projects are > hard. Everybody's pretty busy... > > >> Regarding legal issues, I do not see any problems. >> Is there a web page with instructions or guidelines? I could not find >> anything on the biopython web site. > > The FAQ needs to be updated too! ;) > > Jeff > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > From Y.Benita at pharm.uu.nl Sat May 25 16:12:14 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] New module for analysis of DNA and Protein sequences In-Reply-To: Message-ID: Oh, one more thing. We don't have to write a book. We should have some online documentation describing the different modules, the classes and the methods. Something in the format of the python library. Any new module should have the documentation to go along. Yair on 25/5/2002 10:22, Yair Benita at Y.Benita@pharm.uu.nl wrote: > > Eveybody's always busy. The trick is to split the load between us, not only > those who maintain a module have to write the docs, others can help and it > will be verified later. Writing code that no one knows exist is a waist of > time. Furthermore, documenting should be a continuous process just like > developing. The longer we wait now the harder it will be to write it. > > Yair > > on 24/5/2002 22:29, Jeffrey Chang at jchang@smi.stanford.edu wrote: > >> On Fri, May 24, 2002 at 11:44:52AM +0200, Yair Benita wrote: >>> I also think we should seriously consider revising the documentation of >>> biopython. Many things have changed and if someone wants to know what kind >>> of methods are available in biopython he has to go though the code and read >>> the comments. >> >> I agree. However, maintaining current docs for these projects are >> hard. Everybody's pretty busy... >> >> >>> Regarding legal issues, I do not see any problems. >>> Is there a web page with instructions or guidelines? I could not find >>> anything on the biopython web site. >> >> The FAQ needs to be updated too! ;) >> >> Jeff >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev >> > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > From Y.Benita at pharm.uu.nl Mon May 27 03:34:39 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: Message-ID: on 24/5/02 12:23, Thomas Sicheritz-Ponten at thomas@cbs.dtu.dk wrote: > Anyway, the purpose of sequtils was more like a temporary storage module for > commonly used sequence analyzing utilities/functions. I hoped that most of > the functions would eventually find their way into the modules they > actually should belong too .... > > Whats the overall opinion of sequtils.py? > * Should we reorganize the code and move "movable" functions before > merging/adding PCR modules and documentation? > * Should we use it as it is (maybe after some cosmetic changes) and continue > adding sequence analyzing methods? > * Or, should we split it into core sequence utilities (like GC content and > sequence editing) and more user level defined sequence utilities (like 6 > frame translations, gc skews, graphical GC content etc.) (inherited from > the core module) > > Personally, I'd prefer the latter ... in this case we could have a PCR > module and avoiding duplicated code by putting common functions in the core > sequence utilities module (e.g. GC content, frames etc.) > > Suggestions, ideas, critics??? I suggest 2 different modules: PCR module and Analysis module. The Analysis module will handle everything related to DNA and Protein sequence analysis. The PCR module will use some methods from the analysis module (such as GC content) and will have all methods relevant only to PCR (such as melting temperature). Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From thomas at cbs.dtu.dk Mon May 27 03:31:14 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: References: Message-ID: Yair Benita writes: > on 24/5/02 12:23, Thomas Sicheritz-Ponten at thomas@cbs.dtu.dk wrote: > > > Anyway, the purpose of sequtils was more like a temporary storage module for > > commonly used sequence analyzing utilities/functions. I hoped that most of > > the functions would eventually find their way into the modules they > > actually should belong too .... > > > > Whats the overall opinion of sequtils.py? > > * Should we reorganize the code and move "movable" functions before > > merging/adding PCR modules and documentation? > > * Should we use it as it is (maybe after some cosmetic changes) and continue > > adding sequence analyzing methods? > > * Or, should we split it into core sequence utilities (like GC content and > > sequence editing) and more user level defined sequence utilities (like 6 > > frame translations, gc skews, graphical GC content etc.) (inherited from > > the core module) > > > > Personally, I'd prefer the latter ... in this case we could have a PCR > > module and avoiding duplicated code by putting common functions in the core > > sequence utilities module (e.g. GC content, frames etc.) > > > > Suggestions, ideas, critics??? > > I suggest 2 different modules: PCR module and Analysis module. > The Analysis module will handle everything related to DNA and Protein > sequence analysis. > The PCR module will use some methods from the analysis module (such as GC > content) and will have all methods relevant only to PCR (such as melting > temperature). > Sounds good, but that will leave us still with some functions (currently in sequtils.py) which do not fit completely in either module ... Hmmm, maybe they'll fit in an extra class inside the Analysis module. Jeff a.o., any suggestions for naming and location for the possible PCR and Analysis modules ? cheers -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas@biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From dmitri.gouliaev at telkel.net Mon May 27 05:16:16 2002 From: dmitri.gouliaev at telkel.net (Dmitri I GOULIAEV) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: ; from "Yair Benita" on Mon, May 27, 2002 at 09:34:39AM References: Message-ID: <20020527041616.B22632@lifebook> Hi, Yair Benita ! On Mon, May 27, 2002 at 09:34:39AM +0200, Yair Benita wrote: > I suggest 2 different modules: PCR module and Analysis module. > The Analysis module will handle everything related to DNA and Protein > sequence analysis. > The PCR module will use some methods from the analysis module (such as GC > content) and will have all methods relevant only to PCR (such as melting > temperature). Wow ... This will be quite a module, if you will put EVERYTHING related to DNA and Protein SeqAn into it ... > The PCR module will use some methods from the analysis module (such as GC > content) and will have all methods relevant only to PCR (such as melting > temperature). It is not "relevant ONLY to PCR". Probably, it is not such a bad idea to divide them like this: analysis `-- protein `-- content `-- surface `-- hydrophobicity `-- Kite-Doolittle `-- Eisenberg `-- secondary structure `-- local `-- global `-- nucleic `-- melting temp `-- GC content What's about this: first level -- by object (protein or nucleic sequence), second level -- by what is obtained by this analysis. It's just an idea, the list is not exhaustive. -- DIG (Dmitri I GOULIAEV) All below this line is added by my e-mail provider. From dmitri.gouliaev at telkel.net Mon May 27 05:15:36 2002 From: dmitri.gouliaev at telkel.net (Dmitri I GOULIAEV) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] New module for analysis of DNA and Protein sequences In-Reply-To: ; from "Yair Benita" on Sat, May 25, 2002 at 10:12:14PM References: Message-ID: <20020527041536.A22632@lifebook> Hi, Yair Benita ! On Sat, May 25, 2002 at 10:12:14PM +0200, Yair Benita wrote: > Oh, one more thing. > We don't have to write a book. We should have some online documentation > describing the different modules, the classes and the methods. Something in > the format of the python library. Any new module should have the > documentation to go along. > Yair I agree with you. You have a good point here. -- DIG (Dmitri I GOULIAEV) All below this line is added by my e-mail provider. From Y.Benita at pharm.uu.nl Mon May 27 05:38:29 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: <20020527041616.B22632@lifebook> Message-ID: on 27/5/02 11:16, Dmitri I GOULIAEV at dmitri.gouliaev@telkel.net wrote: > Hi, Yair Benita ! > > On Mon, May 27, 2002 at 09:34:39AM +0200, Yair Benita wrote: > >> I suggest 2 different modules: PCR module and Analysis module. >> The Analysis module will handle everything related to DNA and Protein >> sequence analysis. >> The PCR module will use some methods from the analysis module (such as GC >> content) and will have all methods relevant only to PCR (such as melting >> temperature). > > Wow ... This will be quite a module, if you will put EVERYTHING related to DNA > and Protein SeqAn into it ... > >> The PCR module will use some methods from the analysis module (such as GC >> content) and will have all methods relevant only to PCR (such as melting >> temperature). > > It is not "relevant ONLY to PCR". > > Probably, it is not such a bad idea to divide them like this: > analysis > `-- protein > `-- content > `-- surface > `-- hydrophobicity > `-- Kite-Doolittle > `-- Eisenberg > `-- secondary structure > `-- local > `-- global > `-- nucleic > `-- melting temp > `-- GC content > > What's about this: first level -- by object (protein or nucleic sequence), > second level -- by what is obtained by this analysis. > > It's just an idea, the list is not exhaustive. In my module there are 2 classes: DNA and Protein. The DNA class has access to the Protein class (upon translation of the DNA sequence). Each class has methods of analysis. Basically its not such a big module because many analysis methods are just about listing/summing values of the amino acids along the sequence. Its one method and a different file with all the dictionaries for hydrophobicity, flexibility, MW, etc. I think we should exclude anything related to structure. If we want a module for prediction of secondary structure then it should be a different one. The analysis module will handle only primary structure analysis. Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From dmitri.gouliaev at telkel.net Mon May 27 06:35:07 2002 From: dmitri.gouliaev at telkel.net (Dmitri I GOULIAEV) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: ; from "Yair Benita" on Mon, May 27, 2002 at 11:38:29AM References: <20020527041616.B22632@lifebook> Message-ID: <20020527053507.B23207@lifebook> Hi, Yair Benita ! On Mon, May 27, 2002 at 11:38:29AM +0200, Yair Benita wrote: > In my module there are 2 classes: DNA and Protein. > The DNA class has access to the Protein class (upon translation of the DNA > sequence). I would add the folder ``mixed'' to my hierarchy: seq analysis `-- protein . . . `-- nucleic . . . `-- mixed `-- translation `-- ORF search etc. > Each class has methods of analysis. Basically its not such a big module > because many analysis methods are just about listing/summing values of the > amino acids along the sequence. Its one method and a different file with all > the dictionaries for hydrophobicity, flexibility, MW, etc. > > I think we should exclude anything related to structure. If we want a module > for prediction of secondary structure then it should be a different one. Sure, I agree with you. > The analysis module will handle only primary structure analysis. Ah, OK ! Because, at the first glance to your proposition I saw all the analysis put in one module. I don't think we should make a separation into the modules by complexity of algorithm used. In my opinion, the functionality would be more suitable for this. Best regards, -- DIG (Dmitri I GOULIAEV) All below this line is added by my e-mail provider. From biopython-bugs at bioperl.org Mon May 27 21:22:54 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] Notification: incoming/71 Message-ID: <200205280122.g4S1Msdo012977@pw600a.bioperl.org> JitterBug notification new message incoming/71 Message summary for PR#71 From: "IBRAHIM ANSA" Subject: PARTNERSHIP Date: Tue, 28 May 2002 02:25:00 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From ansaibr110@lycos.com Mon May 27 21:22:54 2002 Received: from bioperl.org ([216.139.166.5]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g4S1MUdo012542 for ; Mon, 27 May 2002 21:22:46 -0400 Message-Id: <200205280122.g4S1MUdo012542@pw600a.bioperl.org> From: "IBRAHIM ANSA" Date: Tue, 28 May 2002 02:25:00 To: biopython-bugs@bioperl.org Subject: PARTNERSHIP MIME-Version: 1.0 Content-Type: text/plain;charset="iso-8859-1" Content-Transfer-Encoding: 7bit UNION BANK PLC STALLION HOUSE MARINA-LAGOS URGENT AND CONFIDENTIAL DEAR SIR, I AM MR. IBARHIM ANSA, THE BILLS AND EXCHANGE DIRECTOR AT THE FOREIGN EXCHANGE REMITTANCE DEPARTMENT OF THE UNION BANK OF NIGERIA PLC, I AM WRITING THIS LETTER TO SOLICIT FOR SUPPORT AND ASSISTANCE FROM YOU TO CARRY OUT THIS BUSINESS OPPORTUINITY IN MY DEPARTMENT. LYING IN AN INACTIVE ACCOUNT IS THE SUM OF $26.5MILLION USD BELONGING TO A FOREIGN CUSTOMER (MR. XAVIER ARIGONI) WHO HAPPENS TO BE DECEASED. HE DIED WITH HIS WIFE AND TWO CHILDREN IN A PLANE CRASH ON BOARD AN ADC AIRLINE FLIGHT AT THE EGIRIN RIVER-LAGOSNIGERIA IN JUNE1998. EVER SINCE HE DIED THE BANK HAS BEEN EXPECTING HIS NEXT OF KIN TO COME AND CLAIM THESE FUNDS. TO THIS EFFECT WE CANNOT RELEASE THE MONEY UNLESS SOMEONE APPLIES FOR IT AS NEXT OF KIN, AS INDICATED IN OUR BANKING GUIDE LINE. UNFORTUNATELY HE HAS NO FAMILY MEMBERS IN NIGERIA OR EUROPE WHO ARE AWARE OF THE EXISTENCE OF THE MONEY (AS HE WAS A CONTRACTOR WITH THE FEDERAL REPUBLIC OF NIGERIA). AT THIS JUNCTURE I HAVE DECIDED TO DO BUSINESS WITH YOU IN COLLABORATION WITH OFFICIALS THAT MATTER IN THE BANK; TO THIS EFFECT WE SOLICIT YOUR HELP IN APPLIYING AS THE NEXT OF KIN THEN THE MONEYWILL BE RELEASED TO YOU. WE DO NOT WANT THIS MONEY TO GO INTO THE BANKS TREASURY AS AN UNCLAIMED BILL. THE BANKING LAW AND GUIDE LINE STIPULATES THAT: IF SUCH MONEY (S) REMAINS UNCLAIMED FOR A PERIOD OF UP TO FOUR YEARS (4YRS) THE MONEY WILL BE TRANSFERRED IN TO THE BANKS TREASURY ASUNCLAIMED FUNDS. OUR REQUEST FOR A FOREIGNER AS NEXT OF KIN IS OCCASIONED BY THE FACT THAT THE CUSTOMER WAS A FOREIGNER AND A NIGERIAN CANNOT STAND AS NEXT OF KIN. SIR, 30 PERCENT OF THE MONEY WILL BE YOUR SHARE AS A FOREIGN PARTNER. THERAFTER MY PARTNERS AND I WILL VISIT YOUR COUNTRY WITH YOUR HELP ONCE THE MONEY HITS YOUR ACCOUNT FOR DISBURSEMENT ACCORDING TO THE PERCENTAGE INDICATED. THEREFORE, TO ENABLE THE IMMEDIATE TRANSFER OF THE FUND TO YOU AS AGREED, YOU MUST APPLY FIRST TO THE BANK AS THE NEXT OF KIN TO THE DECEASED, INDICATING YOUR BANK ACCOUNT NUMBER AND LOCATION WERE THE MONEYWILL BE REMITTED TO. UPON RECEIPT OF YOUR REPLY, I WILL SEND TO YOU BY FAX OR MAIL THE TEXT OF THE APPLICATION AS SOON AS YOU RECEIVE THIS TEXT, I WILL FURTHER CLARIFY YOU IN OTHER ISSUES AS IT AFFECTS THE BUSINESS. BEST REGARDS IBARHIM ANSA From biopython-bugs at bioperl.org Mon May 27 21:49:24 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] Notification: incoming/72 Message-ID: <200205280149.g4S1nOdo015496@pw600a.bioperl.org> JitterBug notification new message incoming/72 Message summary for PR#72 From: "IBRAHIM ANSA" Subject: PARTNERSHIP Date: Tue, 28 May 2002 02:51:04 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From ansaibra110@lycos.com Mon May 27 21:49:24 2002 Received: from bioperl.org ([216.139.166.5]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g4S1mUdo015490 for ; Mon, 27 May 2002 21:48:41 -0400 Message-Id: <200205280148.g4S1mUdo015490@pw600a.bioperl.org> From: "IBRAHIM ANSA" Date: Tue, 28 May 2002 02:51:04 To: biopython-bugs@bioperl.org Subject: PARTNERSHIP MIME-Version: 1.0 Content-Type: text/plain;charset="iso-8859-1" Content-Transfer-Encoding: 7bit UNION BANK PLC STALLION HOUSE MARINA-LAGOS URGENT AND CONFIDENTIAL DEAR SIR, I AM MR. IBARHIM ANSA, THE BILLS AND EXCHANGE DIRECTOR AT THE FOREIGN EXCHANGE REMITTANCE DEPARTMENT OF THE UNION BANK OF NIGERIA PLC, I AM WRITING THIS LETTER TO SOLICIT FOR SUPPORT AND ASSISTANCE FROM YOU TO CARRY OUT THIS BUSINESS OPPORTUINITY IN MY DEPARTMENT. LYING IN AN INACTIVE ACCOUNT IS THE SUM OF $26.5MILLION USD BELONGING TO A FOREIGN CUSTOMER (MR. XAVIER ARIGONI) WHO HAPPENS TO BE DECEASED. HE DIED WITH HIS WIFE AND TWO CHILDREN IN A PLANE CRASH ON BOARD AN ADC AIRLINE FLIGHT AT THE EGIRIN RIVER-LAGOSNIGERIA IN JUNE1998. EVER SINCE HE DIED THE BANK HAS BEEN EXPECTING HIS NEXT OF KIN TO COME AND CLAIM THESE FUNDS. TO THIS EFFECT WE CANNOT RELEASE THE MONEY UNLESS SOMEONE APPLIES FOR IT AS NEXT OF KIN, AS INDICATED IN OUR BANKING GUIDE LINE. UNFORTUNATELY HE HAS NO FAMILY MEMBERS IN NIGERIA OR EUROPE WHO ARE AWARE OF THE EXISTENCE OF THE MONEY (AS HE WAS A CONTRACTOR WITH THE FEDERAL REPUBLIC OF NIGERIA). AT THIS JUNCTURE I HAVE DECIDED TO DO BUSINESS WITH YOU IN COLLABORATION WITH OFFICIALS THAT MATTER IN THE BANK; TO THIS EFFECT WE SOLICIT YOUR HELP IN APPLIYING AS THE NEXT OF KIN THEN THE MONEYWILL BE RELEASED TO YOU. WE DO NOT WANT THIS MONEY TO GO INTO THE BANKS TREASURY AS AN UNCLAIMED BILL. THE BANKING LAW AND GUIDE LINE STIPULATES THAT: IF SUCH MONEY (S) REMAINS UNCLAIMED FOR A PERIOD OF UP TO FOUR YEARS (4YRS) THE MONEY WILL BE TRANSFERRED IN TO THE BANKS TREASURY ASUNCLAIMED FUNDS. OUR REQUEST FOR A FOREIGNER AS NEXT OF KIN IS OCCASIONED BY THE FACT THAT THE CUSTOMER WAS A FOREIGNER AND A NIGERIAN CANNOT STAND AS NEXT OF KIN. SIR, 30 PERCENT OF THE MONEY WILL BE YOUR SHARE AS A FOREIGN PARTNER. THERAFTER MY PARTNERS AND I WILL VISIT YOUR COUNTRY WITH YOUR HELP ONCE THE MONEY HITS YOUR ACCOUNT FOR DISBURSEMENT ACCORDING TO THE PERCENTAGE INDICATED. THEREFORE, TO ENABLE THE IMMEDIATE TRANSFER OF THE FUND TO YOU AS AGREED, YOU MUST APPLY FIRST TO THE BANK AS THE NEXT OF KIN TO THE DECEASED, INDICATING YOUR BANK ACCOUNT NUMBER AND LOCATION WERE THE MONEYWILL BE REMITTED TO. UPON RECEIPT OF YOUR REPLY, I WILL SEND TO YOU BY FAX OR MAIL THE TEXT OF THE APPLICATION AS SOON AS YOU RECEIVE THIS TEXT, I WILL FURTHER CLARIFY YOU IN OTHER ISSUES AS IT AFFECTS THE BUSINESS. BEST REGARDS IBARHIM ANSA From katel at worldpath.net Tue May 28 19:21:37 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] New module for analysis of DNA and Proteinsequences References: Message-ID: <005e01c2069e$6bca1380$08fea8c0@pcklindner> ----- Original Message ----- From: "Yair Benita" To: "Jeffrey Chang" Cc: Sent: Saturday, May 25, 2002 1:22 AM Subject: Re: [Biopython-dev] New module for analysis of DNA and Proteinsequences > > Eveybody's always busy. The trick is to split the load between us, not only > those who maintain a module have to write the docs, others can help and it > will be verified later. Writing code that no one knows exist is a waist of > time. Furthermore, documenting should be a continuous process just like > developing. The longer we wait now the harder it will be to write it. > For parsers a start might be a how-to that explains how to get files, what format the parser expects, what filtering is required and a several line example. Cayte From jchang at smi.stanford.edu Wed May 29 00:42:04 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: <20020527053507.B23207@lifebook>; from dmitri.gouliaev@telkel.net on Mon, May 27, 2002 at 05:35:07AM -0500 References: <20020527041616.B22632@lifebook> <20020527053507.B23207@lifebook> Message-ID: <20020528214203.A81401@springfield.stanford.edu> On Mon, May 27, 2002 at 05:35:07AM -0500, Dmitri I GOULIAEV wrote: > I would add the folder ``mixed'' to my hierarchy: > > seq analysis > `-- protein > . . . > `-- nucleic > . . . > `-- mixed > `-- translation > `-- ORF search This looks reasonable. Thomas (?), go ahead and create a new directory called Bio/SeqAnalysis or Bio/SeqUtils to hold this code. I believe the bioperl equivalent is called SeqUtils. I would prefer not calling it Analysis; it seems too general, especially since we've agreed that this package will not include structure analysis code! Also, when you're integrating code, don't forget to include Bio.Tools.Translate and Bio.Tools.Transcribe modules. Those probably belong in here as well. > I don't think we should make a separation into the modules by > complexity of algorithm used. In my opinion, the functionality would > be more suitable for this. Agreed. Jeff From thomas at cbs.dtu.dk Wed May 29 02:29:45 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PCR module In-Reply-To: <20020528214203.A81401@springfield.stanford.edu> References: <20020527041616.B22632@lifebook> <20020527053507.B23207@lifebook> <20020528214203.A81401@springfield.stanford.edu> Message-ID: Jeffrey Chang writes: > This looks reasonable. Thomas (?), go ahead and create a new > directory called Bio/SeqAnalysis or Bio/SeqUtils to hold this code. I > believe the bioperl equivalent is called SeqUtils. I would prefer not > calling it Analysis; it seems too general, especially since we've > agreed that this package will not include structure analysis code! Ok, I am working on it! Bio/SeqUtils/__init__.py (the funny commented brackets "# {{{" are for emacs fodling mode) How flexible is our genetic code/encoding code? In case anybody has missed it, we got a new amino acid! The 22nd Amino Acid, pyrrolysine is encoded by the RNA nucleotide triplet UAG in archaea. http://www.sciencemag.org/cgi/content/full/296/5572/1409 cheers -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas@biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From thomas at cbs.dtu.dk Wed May 29 02:39:29 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] ThreeLetterProtein In-Reply-To: Message-ID: A question for the ThreeLetterProtein class in Bio/Alphabet/__init__.py: Is there a mapping between the single letter code and the three letter code somewhere? (I don't want to duplicate alphabets ...) cheers -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas@biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From adalke at mindspring.com Thu May 30 02:54:20 2002 From: adalke at mindspring.com (Andrew Dalke) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] ThreeLetterProtein Message-ID: <075201c207a6$d366f220$0301a8c0@josiah.dalkescientific.com> Hej Thomas! >A question for the ThreeLetterProtein class in Bio/Alphabet/__init__.py: >Is there a mapping between the single letter code and the three letter code somewhere? >(I don't want to duplicate alphabets ...) Not really. Only one I could find is in Bio/SCOP/Raf.py (searched for 'GLY') Andrew From jchang at smi.stanford.edu Thu May 30 03:04:09 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] ThreeLetterProtein In-Reply-To: <075201c207a6$d366f220$0301a8c0@josiah.dalkescientific.com>; from adalke@mindspring.com on Thu, May 30, 2002 at 12:54:20AM -0600 References: <075201c207a6$d366f220$0301a8c0@josiah.dalkescientific.com> Message-ID: <20020530000408.A84008@springfield.stanford.edu> On Thu, May 30, 2002 at 12:54:20AM -0600, Andrew Dalke wrote: > Hej Thomas! > > >A question for the ThreeLetterProtein class in Bio/Alphabet/__init__.py: > >Is there a mapping between the single letter code and the three letter code > somewhere? > >(I don't want to duplicate alphabets ...) > > Not really. Only one I could find is in Bio/SCOP/Raf.py > (searched for 'GLY') This sounds like something useful to have. Thomas, can you fit it into the SeqUtils package somewhere? Jeff From thamelry at vub.ac.be Fri May 31 05:42:37 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PDB Parser & Structure object Message-ID: <02053111423704.14634@imolpc112.vub.ac.be> Hi, I added my PDB parser and structure object to the CVS repository. Tests and documentation follow next week. Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode, Belgium http://ultr.vub.ac.be/~thomas From thamelry at vub.ac.be Fri May 31 05:44:25 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:13 2005 Subject: [Biopython-dev] PDB Parser & Structure object Message-ID: <02053111442505.14634@imolpc112.vub.ac.be> > I added my PDB parser and structure object to the CVS > repository. Tests and documentation follow next week. I forgot to mention that the code is in the Bio/PDB directory. -Thomas