From marchywka at hotmail.com Tue Apr 1 10:45:14 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 1 Apr 2008 10:45:14 -0400 Subject: [BiO BB] TopMatch protein structure alignment and superposition web service In-Reply-To: <20080331082118.GF31003@came.sbg.ac.at> References: <20080331082118.GF31003@came.sbg.ac.at> Message-ID: If you use this kind of tool, you may be interested in this relevant test case from Nature today. Could you devise a strategy or find a tool that could have found this similarity? I'm not sure what they mean by "earlier studies" but I assume it wasn't some guy BLAST'ing a 3D databse. You need to register but it is free, http://www.nature.com/nrd/journal/v7/n4/full/nrd2554.html " An important virulence factor in S. aureus is the vivid golden carotenoid pigment staphyloxanthin, which acts as an antioxidant to evade attack by reactive oxygen species from the host immune system. Inhibition of staphyloxanthin biosynthesis is therefore an attractive potential therapeutic strategy to block bacterial infection. Interestingly, earlier studies have noted that the process of staphyloxanthin production is strikingly similar to that of human cholesterol synthesis. Here, using X-ray crystallography, the authors analysed the structure of an essential enzyme involved in the first crucial step of staphyloxanthin biosynthesis: dehydrosqualene synthase (CrtM). They cloned and purified CrtM from S. aureus and revealed that despite only modest sequence homology, it had close structural similarity to human squalene synthase (SQS). This led to the hypothesis that inhibitors of SQS that had already been developed as cholesterol-lowering drugs might also be active against CrtM. " Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Mon, 31 Mar 2008 10:21:18 +0200 > From: markii at came.sbg.ac.at > To: bbb at bioinformatics.org > Subject: [BiO BB] TopMatch protein structure alignment and superposition web service > > We announce the release of TopMatch-web, a public web service for the alignment and superposition of protein structures and the instant > +visualization of structural similiarities. > > We believe that TopMatch is an exceptionally effective, accurate, and enjoyable program for the investigation of protein structure similarities. > > For further information and instructive examples see > Sippl & Wiederstein (2008) > A Note on Difficult Structure Alignment Problems. > Bioinformatics 24, pp. 426-427 > > TopMatch-web is available as a public web service at http://topmatch.services.came.sbg.ac.at. > > Enjoy! > > The TopMatch Team > Center of Applied Molecular Engineering > University of Salzburg > Austria > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008 From skhadar at gmail.com Tue Apr 1 08:57:08 2008 From: skhadar at gmail.com (Shameer Khadar) Date: Tue, 1 Apr 2008 18:27:08 +0530 Subject: [BiO BB] hOW TO LINK TRANSCRIPTION FACTOR TO ITS REGULATED GENES? In-Reply-To: <001a01c8935d$53db9440$bd0211ac@sanger> References: <001a01c8935d$53db9440$bd0211ac@sanger> Message-ID: Which organism you are looking for ? For Drosophila try redfly / flyreg / flytf On Tue, Apr 1, 2008 at 12:00 AM, Mark Tong wrote: > Can any one help me with a database/web site that links known > transcription factor with its regulated genes? > > Thanks in advance, > > Mark > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- K Shameer ========================================= | Indulge | Innovate | Inspire | From hiekeen at gmail.com Tue Apr 1 22:04:36 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Wed, 2 Apr 2008 10:04:36 +0800 Subject: [BiO BB] How to make a network graphic using my genes in pathways? Message-ID: I have 20 pathways. My interesting genes are in these pathways. There are some genes overlaps in these pathways. How can I make a graphic network using these genes? It means connecting these pathways through these overlap genes. What kind of software can I use? Thank you very much in advance. -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com From markii at came.sbg.ac.at Wed Apr 2 04:52:07 2008 From: markii at came.sbg.ac.at (Markus Wiederstein) Date: Wed, 2 Apr 2008 10:52:07 +0200 Subject: [BiO BB] TopMatch protein structure alignment and superposition web service In-Reply-To: References: <20080331082118.GF31003@came.sbg.ac.at> Message-ID: <20080402085207.GF9767@came.sbg.ac.at> Hi Mike, thanks for pointing to this interesting test case. Indeed, the structural similarity of dehydrosqualene synthase (PDB codes: 2zco, 2zcp, 2zcq, 2zcr, 2czs) and humane squalene synthase (PDB codes 1ezf) is striking in the view of their low sequence identity. TopMatch-web yields an RMS of 3.5A and a sequence identity of 11% if the respective chains A are compared. Talking about finding such similarities: one tool that is really helpful for this task is the qCOPS web service (some advertising again ;-) at http://navi.services.came.sbg.ac.at/bin/qCOPS.html For each protein deposited in PDB, you can easily explore its structural neighborhood and visualize structural similarities with TopMatch. If you try with the example you mentioned, you find the dehydrosqualene synthase structures assigned to be similar to 1ezf. For further information on qCOPS, see Sippl et al. A Discrete View on Fold Space Bioinformatics, 24, pp. 870-871 (2008) (Open Access: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn020?ijkey=7zgnEsdKQIEfrN7&keytype=ref) Best regards, -Markus On Die, 01 Apr 2008, Mike Marchywka wrote: > > If you use this kind of tool, you may be interested in this relevant test case from Nature today. > Could you devise a strategy or find a tool that could have found this similarity? > I'm not sure what they mean by "earlier studies" but I assume it wasn't some guy BLAST'ing > a 3D databse. You need to register but it is free, > > http://www.nature.com/nrd/journal/v7/n4/full/nrd2554.html > > > " > > An important virulence factor in S. aureus is the vivid golden carotenoid pigment staphyloxanthin, which acts as an antioxidant to evade attack by reactive oxygen species from the host immune system. Inhibition of staphyloxanthin biosynthesis is therefore an attractive potential therapeutic strategy to block bacterial infection. > > Interestingly, earlier studies have noted that the process of staphyloxanthin production is strikingly similar to that of human cholesterol synthesis. Here, using X-ray crystallography, the authors analysed the structure of an essential enzyme involved in the first crucial step of staphyloxanthin biosynthesis: dehydrosqualene synthase (CrtM). They cloned and purified CrtM from S. aureus and revealed that despite only modest sequence homology, it had close structural similarity to human squalene synthase (SQS). This led to the hypothesis that inhibitors of SQS that had already been developed as cholesterol-lowering drugs might also be active against CrtM. > > " > > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > marchywka at hotmail.com > Note: If I am asking for free stuff, I normally use for hobby/non-profit > information but may use in investment forums, public and private. > Please indicate any concerns if applicable. > Note: Hotmail is possibly blocking my mom's entire > ISP - try me on marchywka at yahoo.com if no reply > here. Thanks. > > > > Date: Mon, 31 Mar 2008 10:21:18 +0200 > > From: markii at came.sbg.ac.at > > To: bbb at bioinformatics.org > > Subject: [BiO BB] TopMatch protein structure alignment and superposition web service > > > > We announce the release of TopMatch-web, a public web service for the alignment and superposition of protein structures and the instant > > +visualization of structural similiarities. > > > > We believe that TopMatch is an exceptionally effective, accurate, and enjoyable program for the investigation of protein structure similarities. > > > > For further information and instructive examples see > > Sippl & Wiederstein (2008) > > A Note on Difficult Structure Alignment Problems. > > Bioinformatics 24, pp. 426-427 > > > > TopMatch-web is available as a public web service at http://topmatch.services.came.sbg.ac.at. > > > > Enjoy! > > > > The TopMatch Team > > Center of Applied Molecular Engineering > > University of Salzburg > > Austria > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > _________________________________________________________________ > Use video conversation to talk face-to-face with Windows Live Messenger. > http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From paolo.romano at istge.it Wed Apr 2 09:19:49 2008 From: paolo.romano at istge.it (Paolo Romano) Date: Wed, 02 Apr 2008 15:19:49 +0200 Subject: [BiO BB] CFP: NETTAB 2008 Message-ID: <200804021330.m32DUjJP014342@ibm43p.biotech.ist.unige.it> ================================= Apologies, if you're receiving multiple copies ================================= Call for Papers for 8th International Workshop NETTAB 2008 NETTAB 2008 Bioinformatics Methods for Biomedical Complex System Applications 19-21 May 2008, Villa Monastero, Varenna, Lake Como, Italy http://www.nettab.org/2008/ The NETTAB 2008 workshop will focus on all aspects needed to provide the framework for understanding multi-scale, complex biological systems, from the single bio-molecule to the cell, across a wide range of clinical information. A special emphasis will be given to combine theory, experiments, software, and technologies for an integrative systems approach to biological research, which is becoming increasingly multi-disciplinary, multi-dimensional, information driven. Sessions Bioinformatics Methods for Complex Systems Gene networking applications Mathematical Methods for System Biology Oncology Bioinformatics Topics (short list) Computational Systems Biology Model-driven development for biological complex systems Software methodologies for complex adaptive systems Multi-agent systems and cellular automata Database integration and data warehouses Analysis of metabolic and regulatory networks Genetic association studies and linkage analysis Proteomics and protein interactions Microarray modelling and analysis Integrative approaches for drug design Grid based and HPC for bioinformatics applications For the full list of topics please consult the NETTAB web site. Tutorials Systems Biology Tools Systems Biology Standards Important dates 10 April 2008: Paper submission 21 April 2008: Communication of acceptance 22 April 2008: Registration starts 19 May 2008: Tutorials 19-21 May 2008: Workshop Abstracts' submission Submit an extended abstract (max 3 pages) within next 10 April 2008. Guidelines and instructions for submission are available at: http://www.nettab.org/call.html . A MS Word template is available at: http://www.nettab.org/2008/abstract.doc . Registration Registration opens on 22 April 2008. Register for the NETTAB 2008 workshop: http://www.nettab.org/2008/rform.html For all information, please email to nettab2008 at itb.cnr.it . Chairs Luciano Milanesi, Institute of Biomedical Technologies, National Research Council, Milan, Italy Paolo Romano, Bioinformatics, National Cancer Research Institute, Genoa, Italy Scientific Committee Lilia Alberghina, University of Milan Bicocca, Italy Alberto Albertini, CNR-ITB, Milano, Italy Claudia Angelini, CNR-IAC, Napoli, Italy Francesco Beltrame, ICT Department, CNR, Rome, Italy Paola Bertolazzi, CNR-IASI, Rome, Italy Flavio Corradini, University of Camerino, Italy Nicola Cannata, University of Camerino, Italy Luca Cardelli, Microsoft Research, Cambridge UK Rita Casadio, University of Bologna, Italy Gastone Castellani, University of Bologna, Italy Gianluigi Condorelli, Medical Department, CNR, Rome, Italy Daniele Cusi, University of Milan, Italy Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France Angelo Facchiano, CNR-ISA, Avellino, Italy Piero Fariselli, University of Bologna, Italy Raffaele Giancarlo, University of Palermo, Italy Radu Grosu, State University of New YorkStony Brook, USA Liliana Ironi, CNR-IMATI, Pavia, Italy Alexander Kel, Biobase, Germany Pietro Li?, University of Cambridge, UK Fabio Macciardi, University of Milan, Italy Roberto Marangoni, University of Pisa, Italy Francesco Masulli, University of Genoa, Italy Giancarlo Mauri, University of Milan Bicocca, Italy Emanuela Merelli, University of Camerino, Italy Andrey Mironov, Moscow University, Russia Marco Muselli, CNR, Genoa, Italy Giovanni Paolella, CEINGE, University of Naples, Itlay Marco Pellegrini, CNR-IIT, Pisa Italy Annibale Puca, Multimedica, Milano, Italy Scott Smolka, State University of New York Stony Brook, USA Roberto Tagliaferri, University of Salento, Italy Giorgio Valentini, University of Milan, Italy We are looking forward to meeting you at NETTAB 2008 in Varenna! Best regards. On behalf of the Organizing Committee Paolo Romano Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 Skype: p.romano Web: http://www.nettab.org/promano/ From pandey.gaurav at gmail.com Wed Apr 2 18:49:59 2008 From: pandey.gaurav at gmail.com (Gaurav Pandey) Date: Wed, 2 Apr 2008 17:49:59 -0500 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: References: Message-ID: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> You can try GraphViz (http://www.graphviz.org/). Gaurav On Tue, Apr 1, 2008 at 9:04 PM, Jinyan Huang wrote: > I have 20 pathways. My interesting genes are in these pathways. There > are some genes overlaps in these pathways. How can I make a graphic > network using these genes? It means connecting these pathways through > these overlap genes. What kind of software can I use? > > Thank you very much in advance. > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Gaurav Pandey Email: gaurav at cs.umn.edu Computer Science Department Webpage: www.cs.umn.edu/~gaurav University of Minnesota Tel: 612-701-2494 From jakechen at iupui.edu Wed Apr 2 23:54:29 2008 From: jakechen at iupui.edu (Chen, Jake) Date: Wed, 2 Apr 2008 23:54:29 -0400 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: References: Message-ID: <602F0EFD9E534C4EBBBC6502A8EA501B042C97CCB0@iu-mssg-mbx06.ads.iu.edu> Dear Jinyan, We have a software tool called "ProteoLens" (http://bio.informatics.iupui.edu/proteolens/) that is quite robust, especially if you are familiar with SQL and would like to use Oracle , postgreSQL, or GML to manage your network data. For a simple network with prettier layout and click-style navigator, try Cytoscape. Best, Jake Chen, Ph.D. Assistant Professor, (IU) Informatics & (Purdue) Computer Science Director, Indiana Center for Systems Biology and Personalized Medicine Indiana University - Purdue University Indianapolis 719 Indiana Avenue, WK #190 Indianapolis, IN 46202 Office: (317) 278-7604 Lab: (317) 274-7542 jakechen at iupui.edu | http://bio.informatics.iupui.edu/ -----Original Message----- From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] On Behalf Of Jinyan Huang Sent: Tuesday, April 01, 2008 10:05 PM To: bbb at bioinformatics.org Subject: [BiO BB] How to make a network graphic using my genes in pathways? I have 20 pathways. My interesting genes are in these pathways. There are some genes overlaps in these pathways. How can I make a graphic network using these genes? It means connecting these pathways through these overlap genes. What kind of software can I use? Thank you very much in advance. -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From eddiekok at yahoo.com Thu Apr 3 01:54:00 2008 From: eddiekok at yahoo.com (eddie kok) Date: Thu, 3 Apr 2008 16:54:00 +1100 (EST) Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: Message-ID: <460852.33034.qm@web54503.mail.re2.yahoo.com> Dear Jinyan, You may want to try this website: http://www.genome.jp/kegg/tool/search_pathway.html Thanks. Best regards, eddie Jinyan Huang wrote: I have 20 pathways. My interesting genes are in these pathways. There are some genes overlaps in these pathways. How can I make a graphic network using these genes? It means connecting these pathways through these overlap genes. What kind of software can I use? Thank you very much in advance. -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb --------------------------------- Get the name you always wanted with the new y7mail email address. From schreibe at ipk-gatersleben.de Thu Apr 3 02:05:36 2008 From: schreibe at ipk-gatersleben.de (Falk Schreiber) Date: Thu, 03 Apr 2008 08:05:36 +0200 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> References: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> Message-ID: <47F473B0.9090209@ipk-gatersleben.de> Hello, you could also try Vanted (http://vanted.ipk-gatersleben.de). You can load/copy all pathways in one view and then simply merge multiple occurances of the same elements (genes) into one element. Kind regards Falk Gaurav Pandey wrote: > You can try GraphViz (http://www.graphviz.org/). > > Gaurav > > On Tue, Apr 1, 2008 at 9:04 PM, Jinyan Huang wrote: > >> I have 20 pathways. My interesting genes are in these pathways. There >> are some genes overlaps in these pathways. How can I make a graphic >> network using these genes? It means connecting these pathways through >> these overlap genes. What kind of software can I use? >> >> Thank you very much in advance. >> >> >> -- >> Best regards, >> Jinyan Huang (ekeen) >> School of Life Sciences and Technology, 1302 Room >> Tongji University >> Siping Road 1239, Shanghai 200092 >> P.R. China >> Tel :0086-21-65981041 >> Msn: hiekeen at hotmail.com >> eMail: hiekeen at gmail.com >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > -- Prof. Dr. Falk Schreiber http://bic-gh.ipk-gatersleben.de/~schreibe/ From timothydoconnor at gmail.com Thu Apr 3 03:02:01 2008 From: timothydoconnor at gmail.com (Timothy O'Connor) Date: Thu, 3 Apr 2008 01:02:01 -0600 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> References: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> Message-ID: I recommend cytoscape: http://www.cytoscape.org/. I haven't done it yet but it seems to be set up to run analyses as well. The pictures come out pretty good as well. Tim On Wed, Apr 2, 2008 at 4:49 PM, Gaurav Pandey wrote: > You can try GraphViz (http://www.graphviz.org/). > > Gaurav > > > > On Tue, Apr 1, 2008 at 9:04 PM, Jinyan Huang wrote: > > > I have 20 pathways. My interesting genes are in these pathways. There > > are some genes overlaps in these pathways. How can I make a graphic > > network using these genes? It means connecting these pathways through > > these overlap genes. What kind of software can I use? > > > > Thank you very much in advance. > > > > > > -- > > Best regards, > > Jinyan Huang (ekeen) > > School of Life Sciences and Technology, 1302 Room > > Tongji University > > Siping Road 1239, Shanghai 200092 > > P.R. China > > Tel :0086-21-65981041 > > Msn: hiekeen at hotmail.com > > eMail: hiekeen at gmail.com > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > Gaurav Pandey Email: gaurav at cs.umn.edu > Computer Science Department Webpage: www.cs.umn.edu/~gaurav > University of Minnesota Tel: 612-701-2494 > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From ahmed.essaghir at gmail.com Thu Apr 3 05:27:07 2008 From: ahmed.essaghir at gmail.com (ahmed essaghir) Date: Thu, 3 Apr 2008 11:27:07 +0200 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> References: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> Message-ID: <6ec4c2000804030227h515ffca8t52d2d9abad8c89f6@mail.gmail.com> hi! you can use Cytoscape www.cytoscape.org you can create your pathways graph by creating a .sif file (it's easy) a .sif file is a tab delimited one in which you have three columns : the first column contains the start nodes id and the second cotains an abreviation standing for the type of relationship between your nodes (pp for protein-protein, pr for protein-reaction, ...) and the third column contains the target nodes id : example : let's assume you havz a pathway like this in which a, b, c, d are proteins ids, so the relationship is "pp" a ----> b ----> c ---> d d---> b then your sif file will be like this a tabSpace b b tabSpace c c tabSpace d d tabSpace b then you can open your graph using cytoscape and if you want to map you nodes (genes) in the graph you just do "select node from a file" (a file containing you genes of interest in the same ids of course as you used in the graph) then you'll have your genes hilighted where ever they are in the graph. also you can edit your graph in a user friendly way by deleting and adding arcs and nodes. you have also some plugins that allow you to highlight your genes according to their expression (if you have microarray data expression). have fun From skhadar at gmail.com Thu Apr 3 09:00:55 2008 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 3 Apr 2008 18:30:55 +0530 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: References: Message-ID: Why dont you check BioRuby ? I think they have a couple of classes to map genes on to KEGG pathway. http://bioruby.open-bio.org/ Cheers, Shameer NCBS _ TIFR On Wed, Apr 2, 2008 at 7:34 AM, Jinyan Huang wrote: > I have 20 pathways. My interesting genes are in these pathways. There > are some genes overlaps in these pathways. How can I make a graphic > network using these genes? It means connecting these pathways through > these overlap genes. What kind of software can I use? > > Thank you very much in advance. > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- K Shameer ========================================= | Indulge | Innovate | Inspire | From marchywka at hotmail.com Thu Apr 3 17:35:12 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 3 Apr 2008 17:35:12 -0400 Subject: [BiO BB] TopMatch protein structure alignment and superposition web service In-Reply-To: <20080402085207.GF9767@came.sbg.ac.at> References: <20080331082118.GF31003@came.sbg.ac.at> <20080402085207.GF9767@came.sbg.ac.at> Message-ID: > For each protein deposited in PDB, you can easily explore its structural neighborhood and visualize structural similarities with TopMatch. > If you try with the example you mentioned, you find the dehydrosqualene synthase structures assigned to be similar to 1ezf. Sure, if you have suspects I guess this is helpful. I was thinking of something like a cavity or surface database however. I guess in this case, you could suspect functional similarities but I don't know if there is something to compare shape and chemical environments of cavities. I wrote some cavity code for my home-made molecule viewer and was able to generate some nice pictures by coloring cavity walls based on nearest atom type, but I'm not sure if something like that would be useful for finding related enzymes. I'll have to get the sequences and see if my rule annotater can find functional similarities in 1D when I get a chance. Are there known, conserved functional groups in 1D that help create the 3D structure even if this amounts to limited total sequence identity? > Date: Wed, 2 Apr 2008 10:52:07 +0200 > From: markii at came.sbg.ac.at > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] TopMatch protein structure alignment and superposition web service > > Hi Mike, > > thanks for pointing to this interesting test case. > > Indeed, the structural similarity of dehydrosqualene synthase (PDB codes: 2zco, 2zcp, 2zcq, 2zcr, 2czs) and humane squalene synthase (PDB codes 1ezf) is striking in the view of their low sequence identity. TopMatch-web yields an RMS of 3.5A and a sequence identity of 11% if the respective chains A are compared. > > Talking about finding such similarities: one tool that is really helpful for this task is the qCOPS web service (some advertising again ;-) at > http://navi.services.came.sbg.ac.at/bin/qCOPS.html > > For each protein deposited in PDB, you can easily explore its structural neighborhood and visualize structural similarities with TopMatch. > If you try with the example you mentioned, you find the dehydrosqualene synthase structures assigned to be similar to 1ezf. > > For further information on qCOPS, see > Sippl et al. > A Discrete View on Fold Space > Bioinformatics, 24, pp. 870-871 (2008) > (Open Access: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn020?ijkey=7zgnEsdKQIEfrN7&keytype=ref) > > Best regards, > -Markus > _________________________________________________________________ Pack up or back up?use SkyDrive to transfer files or keep extra copies. Learn how. hthttp://www.windowslive.com/skydrive/overview.html?ocid=TXT_TAGLM_WL_Refresh_skydrive_packup_042008 From srikrishnamohan at gmail.com Fri Apr 4 03:04:49 2008 From: srikrishnamohan at gmail.com (km) Date: Fri, 4 Apr 2008 12:34:49 +0530 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: References: Message-ID: Hi, take a peek at the biocyc.org website and the screencasts over there. http://biocyc.org/webinar.shtml that should enable u to do the same. KM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Wed, Apr 2, 2008 at 7:34 AM, Jinyan Huang wrote: > I have 20 pathways. My interesting genes are in these pathways. There > are some genes overlaps in these pathways. How can I make a graphic > network using these genes? It means connecting these pathways through > these overlap genes. What kind of software can I use? > > Thank you very much in advance. > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From hlapp at gmx.net Fri Apr 4 22:13:00 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 4 Apr 2008 22:13:00 -0400 Subject: [BiO BB] Last Call for Student Applications - Google Summer of Code In-Reply-To: <89B3A0C3-444C-40AA-B8BD-50D117B27799@gmx.net> References: <89B3A0C3-444C-40AA-B8BD-50D117B27799@gmx.net> Message-ID: <42995184-C7ED-482B-9A41-308B8B40A687@gmx.net> The National Evolutionary Synthesis Center (NESCent: http:// www.nescent.org/) is participating in the 2008 Google Summer of Code, see below for the previous announcement. This is just a reminder that the student application period ends definitively on April 7 (Monday), 5pm PDT/8pm EDT (0:00 UTC on April 8). (Google extended the period from the original end date of March 31.) There are still a few project ideas that have received little attention from student applications so far. If you are interested, please see below for URLs, and get in touch with us phylosoc {at} nescent {dot} org to inquire for more information re: application status of your favorite project(s). -hilmar On Mar 28, 2008, at 10:38 AM, Hilmar Lapp wrote: Phyloinformatics Summer of Code 2008 http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008 *** Please disseminate this announcement widely to appropriate students at your institution *** The National Evolutionary Synthesis Center (NESCent: http:// www.nescent.org/) is participating in 2008 for the second year as a mentoring organization in the Google Summer of Code (http:// code.google.com/soc). Through this program, Google provides undergraduate, masters, and PhD students with a unique opportunity to obtain hands-on experience writing and extending open-source software under the mentorship of experienced developers from around the world. Our goal in participating is to train future researchers and developers to not only have awareness and understanding of the value of open-source and collaboratively developed software, but also to gain the programming and remote collaboration skills needed to successfully contribute to such projects. Students will receive a stipend from Google, and may work from their home, or home institution, for the duration of the 3 month program. Students will each have one or more dedicated mentors with expertise in phylogenetic methods and open-source software development. NESCent is particularly targeting students interested in both evolutionary biology and software development. Project ideas (see URL below) range from visualizing phylogenetic data in R, to development of a Mesquite module, web-services for phylogenetic data providers or geophylogeny mashups, implementing phyloXML support, navigating databases of networks, topology queries for PhyloCode registries, to phylogenetic tree mining in a MapReduce framework, and more. The project ideas are flexible and many can be adjusted in scope to match the skills of the student. If the program sounds interesting to you but you are unsure whether you have the necessary skills, please email the mentors at the address below. We will work with you to find a project that fits your interests and skills. INQUIRIES: Email any questions, including self-proposed project ideas, to phylosoc {at} nescent {dot} org. TO APPLY: Apply on-line at the Google Summer of Code website (http://code.google.com/soc/2008), where you will also find GSoC program rules and eligibility requirements. The 1-week application period for students opened on Monday March 24th and runs through Monday, March 31st, 2008. Hilmar Lapp and Todd Vision US National Evolutionary Synthesis Center ===== URLs: ===== 2008 NESCent Phyloinformatics Summer of Code: http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008 Eligibility requirements: http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_eligibility Stipends: http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_administrivia To sign up for quarterly NESCent newsletters: with announcements about upcoming programs at the Center: http://www.nescent.org/about/contact.php _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From ekeen at mail.tongji.edu.cn Mon Apr 7 02:56:08 2008 From: ekeen at mail.tongji.edu.cn (Jinyan Huang) Date: Mon, 7 Apr 2008 14:56:08 +0800 Subject: [BiO BB] How to analysis the relationship of my interesting KEGG pathways? Message-ID: In my research, I got 25 interesting pathways. I want to know the regulated relationship of these pathways. It is better if there some software to connect these KEGG pathways. Thank you very much in advance. From schreibe at ipk-gatersleben.de Tue Apr 8 01:51:22 2008 From: schreibe at ipk-gatersleben.de (Falk Schreiber) Date: Tue, 08 Apr 2008 07:51:22 +0200 Subject: [BiO BB] How to analysis the relationship of my interesting KEGG pathways? In-Reply-To: References: Message-ID: <47FB07DA.5050303@ipk-gatersleben.de> Hello, you could try KGML-ED (http://kgml-ed.ipk-gatersleben.de/Introduction.html), a tool that allows the dynamic exploration, combination and editing of KEGG Pathway diagrams. It is a graphical network editor, that provides read- and write-support for the KGML (KEGG Markup Language) file format. Kind regards Falk Jinyan Huang wrote: > In my research, I got 25 interesting pathways. I want to know the > regulated relationship of these pathways. It is better if there some > software to connect these KEGG pathways. > > Thank you very much in advance. > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Prof. Dr. Falk Schreiber http://bic-gh.ipk-gatersleben.de/~schreibe/ From kcallenb at email.sjsu.edu Wed Apr 9 03:07:47 2008 From: kcallenb at email.sjsu.edu (Keith Callenberg) Date: Wed, 9 Apr 2008 00:07:47 -0700 Subject: [BiO BB] Advanced web query interfaces for biological databases Message-ID: I am working on the web interface for a fairly complex database that integrates several different types of data (gene expression, sequence, annotation). A basic interface for accessing individual records in the database has already been written, but my lab's biologists would like to see a more powerful form interface. They would like to be able to add thresholds on arbitrary fields and set other parameters for several fields at a time. I have been pointed to the Query Builder on NCBI's Trace Archive (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) as the basic concept, and I can see how that could be implemented with its helpful auto-complete text, but it seems like it still has quite a learning curve and is not really very intuitive. I have also found BioCyc.org's Advanced Query page (http://biocyc.org/query.html) and several others that are similar or harder to use. AJAX can help, and we plan to integrate auto-completion of some text, but I would like to build something powerful and yet intuitive that does not require someone to read a manual before using. Any suggestions? I suppose innovation in UI design often starts in other places first so I'd appreciate any non-biological examples as well. Thanks! Keith Callenberg From Sterten at aol.com Wed Apr 9 11:53:48 2008 From: Sterten at aol.com (Sterten at aol.com) Date: Wed, 9 Apr 2008 11:53:48 EDT Subject: [BiO BB] Advanced web query interfaces for biological databases Message-ID: IMO it's better if people download the whole database and then run applications offline From marchywka at hotmail.com Wed Apr 9 12:58:08 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 9 Apr 2008 12:58:08 -0400 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: As I suggest to anyone who will listen, provide an API ( a machine usable interface) to let third parties ( as well as yourself ) design whatever UI's you determine make sense. Any complicated data source is best accessed programmatically and a web interface is only useful for the casual user doing one-of situations or exploratory work. In some cases, this may be the full extent of the immediate need. Unless you think are can anticipate every need that every user may have with your data source, an API that exposes all the data that you are willing to reveal is the best way to go. So, I'd recommend publishing an API and even sample scripts for your own developers first and then worry about some specialized web interfaces. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Wed, 9 Apr 2008 00:07:47 -0700 > From: kcallenb at email.sjsu.edu > To: bbb at bioinformatics.org > Subject: [BiO BB] Advanced web query interfaces for biological databases > > I am working on the web interface for a fairly complex database that > integrates several different types of data (gene expression, sequence, > annotation). A basic interface for accessing individual records in the > database has already been written, but my lab's biologists would like > to see a more powerful form interface. They would like to be able to > add thresholds on arbitrary fields and set other parameters for > several fields at a time. > > I have been pointed to the Query Builder on NCBI's Trace Archive > (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) as the basic concept, > and I can see how that could be implemented with its helpful > auto-complete text, but it seems like it still has quite a learning > curve and is not really very intuitive. I have also found BioCyc.org's > Advanced Query page (http://biocyc.org/query.html) and several others > that are similar or harder to use. AJAX can help, and we plan to > integrate auto-completion of some text, but I would like to build > something powerful and yet intuitive that does not require someone to > read a manual before using. Any suggestions? I suppose innovation in > UI design often starts in other places first so I'd appreciate any > non-biological examples as well. > > Thanks! > > Keith Callenberg > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Pack up or back up?use SkyDrive to transfer files or keep extra copies. Learn how. hthttp://www.windowslive.com/skydrive/overview.html?ocid=TXT_TAGLM_WL_Refresh_skydrive_packup_042008 From skhadar at gmail.com Wed Apr 9 13:41:34 2008 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 9 Apr 2008 23:11:34 +0530 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: It will be an interesting UI design. Now many bioinformatics web resources are coming up with intuitive use of js libraries like YUI, scriptaculous etc. Flex is also an excellent tool for revolutionary UI development. If I were you, I would have used a combination of js library + flex thats my 2 cents cheers, Shameer On Wed, Apr 9, 2008 at 12:37 PM, Keith Callenberg wrote: > I am working on the web interface for a fairly complex database that > integrates several different types of data (gene expression, sequence, > annotation). A basic interface for accessing individual records in the > database has already been written, but my lab's biologists would like > to see a more powerful form interface. They would like to be able to > add thresholds on arbitrary fields and set other parameters for > several fields at a time. > > I have been pointed to the Query Builder on NCBI's Trace Archive > (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) as the basic concept, > and I can see how that could be implemented with its helpful > auto-complete text, but it seems like it still has quite a learning > curve and is not really very intuitive. I have also found BioCyc.org's > Advanced Query page (http://biocyc.org/query.html) and several others > that are similar or harder to use. AJAX can help, and we plan to > integrate auto-completion of some text, but I would like to build > something powerful and yet intuitive that does not require someone to > read a manual before using. Any suggestions? I suppose innovation in > UI design often starts in other places first so I'd appreciate any > non-biological examples as well. > > Thanks! > > Keith Callenberg > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- K Shameer ========================================= | Indulge | Innovate | Inspire | From barry.hardy at vtxmail.ch Thu Apr 10 08:46:33 2008 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Thu, 10 Apr 2008 14:46:33 +0200 Subject: [BiO BB] Bursary Award for eCheminfo Hands-on Drug Discovery Workshop in Oxford Message-ID: <47FE0C29.4080900@vtxmail.ch> We will be accepting academic Bursary Award submissions for attending the eCheminfo Hands-on Drug Discovery Workshop in Oxford through Friday April 18. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com Selection will be based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on the research. We gratefully acknowledge the Bursary sponsorship support of Tripos. The 5 Day Workshop Week will take place this year 21-25 July 2008 at the Medical Sciences Teaching Center, Oxford University, Oxford, UK. Topics to be covered include Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling. The workshop group will study problems with hands-on examples using a range of software methods and will discuss complex issues highlighted by the exercises and case studies presented by instructors. A variety of leading drug discovery software packages and an IT classroom are used by instructors and participants to work through problems. More Information: Web: http://echeminfo.colayer.net/COMTY_training Blog: http://barryhardy.blogs.com/cheminfostream/2008/03/drug-discovery.html Photos: http://echeminfo.com/COMTY_oxfordphotos06 best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Switzerland Tel: +41 61 851 0170 From info at bioinformaticsworldwide.com Thu Apr 10 14:22:04 2008 From: info at bioinformaticsworldwide.com (Bioinformatics World Wide) Date: Thu, 10 Apr 2008 13:22:04 -0500 Subject: [BiO BB] New Bioinformatics Community world wide - Invitation Message-ID: Dear Scientist, This is an invitation to join Bioinformatics World Wide (http://www.bioinformaticsworldwide.com), a community maintained web site dedicated to the fields of Bioinformatics and Computational Biology. This is an open community to people working in or with Bioinformatics related field. On this site you shall find: * News postings about the goings on in the field * Job and studentship adverts that our users have found and submitted to the site * A calendar/event list detailing upcoming events relevant to the fields * Active forums for people to come and ask for help or for a chat * Each member can create groups, invite friends and find online help through our chat rooms. * Each member can personnalize his homepage and create his own bioinformatics Blog We hope that you find the site a useful resource and encourage you to join us and to ask your friends do the same. This site is made for you and will be enriched by you. Looking forward to see you in BWW. BWW Administrator From kcallenb at email.sjsu.edu Sun Apr 13 20:47:05 2008 From: kcallenb at email.sjsu.edu (Keith Callenberg) Date: Sun, 13 Apr 2008 17:47:05 -0700 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: Shameer, thank you for you suggestions. I have heard good things about Flex's UI capabilities and I will check it out. I think many people's concept of the web is limited by a notion that scripting languages like php, ruby, python and perl are as far as we can go within the browser. I think it will take a combination of new technologies -- perhaps a combination like the one you've suggested -- to go further. Keith On Wed, Apr 9, 2008 at 10:41 AM, Shameer Khadar wrote: > It will be an interesting UI design. > Now many bioinformatics web resources are coming up with intuitive use of js > libraries like YUI, scriptaculous etc. Flex is also an excellent tool for > revolutionary UI development. If I were you, I would have used a combination > of js library + flex > > thats my 2 cents > cheers, > Shameer > > On Wed, Apr 9, 2008 at 12:37 PM, Keith Callenberg > wrote: > > > > > I am working on the web interface for a fairly complex database that > > integrates several different types of data (gene expression, sequence, > > annotation). A basic interface for accessing individual records in the > > database has already been written, but my lab's biologists would like > > to see a more powerful form interface. They would like to be able to > > add thresholds on arbitrary fields and set other parameters for > > several fields at a time. > > > > I have been pointed to the Query Builder on NCBI's Trace Archive > > (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) as the basic concept, > > and I can see how that could be implemented with its helpful > > auto-complete text, but it seems like it still has quite a learning > > curve and is not really very intuitive. I have also found BioCyc.org's > > Advanced Query page (http://biocyc.org/query.html) and several others > > that are similar or harder to use. AJAX can help, and we plan to > > integrate auto-completion of some text, but I would like to build > > something powerful and yet intuitive that does not require someone to > > read a manual before using. Any suggestions? I suppose innovation in > > UI design often starts in other places first so I'd appreciate any > > non-biological examples as well. > > > > Thanks! > > > > Keith Callenberg > > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > K Shameer > ========================================= > | Indulge | Innovate | Inspire | > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From keithcallenberg at gmail.com Sun Apr 13 20:23:30 2008 From: keithcallenberg at gmail.com (Keith Callenberg) Date: Sun, 13 Apr 2008 17:23:30 -0700 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: Thanks for your suggestion, Mike. As a developer I also value the concept of an open and freely available API, and I wish that more sites would provide these, but I am not sure it is yet appropriate for our database as it will be some time before we have a sizable pool of users, letalone developers. Also, I might not be clear on what you mean by "programmatically," but I think it is a bit short-sighted to limit the scope of web-based interfaces to only casual queries. I am not usually a supporter of the term "Web 2.0" because I think it has lately signified little more than colorful buttons, but I do believe more and more tasks can be accomplished from within the browser. I believe energy should be put into moving more advanced tasks online because it removes learning curves and hardware restrictions, thereby increasing your base of users. I think it is not easy to develop an intuitive web-based UI that is not fairly restrictive, but that does not mean it should not be pursued. Keith On Wed, Apr 9, 2008 at 9:58 AM, Mike Marchywka wrote: > > > > As I suggest to anyone who will listen, provide an API ( a machine usable interface) to let > third parties ( as well as yourself ) design whatever UI's you determine make sense. > Any complicated data source is best accessed programmatically and a web interface is only > useful for the casual user doing one-of situations or exploratory work. In some cases, > this may be the full extent of the immediate need. Unless you think are can anticipate > every need that every user may have with your data source, an API that exposes all > the data that you are willing to reveal is the best way to go. > > So, I'd recommend publishing an API and even sample scripts for your own developers > first and then worry about some specialized web interfaces. > > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > marchywka at hotmail.com > Note: If I am asking for free stuff, I normally use for hobby/non-profit > information but may use in investment forums, public and private. > Please indicate any concerns if applicable. > Note: Hotmail is possibly blocking my mom's entire > ISP - try me on marchywka at yahoo.com if no reply > here. Thanks. > > > > Date: Wed, 9 Apr 2008 00:07:47 -0700 > > From: kcallenb at email.sjsu.edu > > To: bbb at bioinformatics.org > > Subject: [BiO BB] Advanced web query interfaces for biological databases > > > > > > I am working on the web interface for a fairly complex database that > > integrates several different types of data (gene expression, sequence, > > annotation). A basic interface for accessing individual records in the > > database has already been written, but my lab's biologists would like > > to see a more powerful form interface. They would like to be able to > > add thresholds on arbitrary fields and set other parameters for > > several fields at a time. > > > > I have been pointed to the Query Builder on NCBI's Trace Archive > > (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) as the basic concept, > > and I can see how that could be implemented with its helpful > > auto-complete text, but it seems like it still has quite a learning > > curve and is not really very intuitive. I have also found BioCyc.org's > > Advanced Query page (http://biocyc.org/query.html) and several others > > that are similar or harder to use. AJAX can help, and we plan to > > integrate auto-completion of some text, but I would like to build > > something powerful and yet intuitive that does not require someone to > > read a manual before using. Any suggestions? I suppose innovation in > > UI design often starts in other places first so I'd appreciate any > > non-biological examples as well. > > > > Thanks! > > > > Keith Callenberg > > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > _________________________________________________________________ > Pack up or back up?use SkyDrive to transfer files or keep extra copies. Learn how. > hthttp://www.windowslive.com/skydrive/overview.html?ocid=TXT_TAGLM_WL_Refresh_skydrive_packup_042008 > _______________________________________________ > > > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From marchywka at hotmail.com Mon Apr 14 07:27:11 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 14 Apr 2008 07:27:11 -0400 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: If you are really sold on a fancy UI and wish to consider the other poster's "download the whole database idea" and allow automated access without lots of repeated code versions, java is the obvious choice for everything. An applet for the browser is easily invoked standalone with little additional effort. Java is fast enough for most UI's and has the flexibility for a programming language with lots of built in UI support. This may sound a bit silly but I also wouldn't dismiss support for mobile phones. I used to find myself surfing pubmed or otherwise looking into stuff while on the freeway or waiting in various locations. If you have something which is well treated with a GUI that looks like a video game, maybe it would be a natural spare time activity on mobile devices :) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Wed, 9 Apr 2008 23:11:34 +0530 > From: skhadar at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] Advanced web query interfaces for biological databases > > It will be an interesting UI design. > Now many bioinformatics web resources are coming up with intuitive use of js > libraries like YUI, scriptaculous etc. Flex is also an excellent tool for > revolutionary UI development. If I were you, I would have used a combination > of js library + flex > > thats my 2 cents > cheers, > Shameer > _________________________________________________________________ Pack up or back up?use SkyDrive to transfer files or keep extra copies. Learn how. hthttp://www.windowslive.com/skydrive/overview.html?ocid=TXT_TAGLM_WL_Refresh_skydrive_packup_042008 From tavishmit at gmail.com Mon Apr 14 11:10:31 2008 From: tavishmit at gmail.com (Tavish Baker) Date: Mon, 14 Apr 2008 11:10:31 -0400 Subject: [BiO BB] Multicore Programming / Network Coding Message-ID: Hi All, Based on some of the posts I have seen over the year, I thought this might be of interest to some of you. MIT will be holding some computing / network short courses on campus this summer, maybe of particular interest to you all are: Multicore Programming July 14-18, 2008 http://web.mit.edu/mitpep/pi/courses/multicore_programming.html The course exposes students to fundamental issues in the design of concurrent programs and to the techniques necessary to make effective use of multicore machines. It combines lectures and classwork to gradually enhance students' intuition and technique. And maybe... Introduction to Network Coding August 4-8, 2008 http://web.mit.edu/mitpep/pi/courses/network_coding.html Network coding is a new area of networking, in which data is manipulated inside the network to increase throughput, reduce delay, and improve robustness. This field has recently found commerical applications in content distribution, peer-to-peer design, and enabling high-throughput wireless networks. The goal of this class is to provide participants with the theoretical and practical tools necessary not only to understand the field of network coding, but also to conduct independent, innovative work in the area. The curriculum reflects this mixture of theoretical foundations and practical approaches. From marchywka at hotmail.com Mon Apr 14 13:16:16 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 14 Apr 2008 13:16:16 -0400 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: > our database as it will be some time before we have a sizable pool of > users, letalone developers. And what kind of interface will your few developers use? I guess my point is that if you have a compelling data set, developers will come out of the wood work to support it. > Also, I might not be clear on what you mean by "programmatically," but > I think it is a bit short-sighted to limit the scope of web-based > interfaces to only casual queries. I'm not advocating intentional limitations, just expressing the problem with a GUI. You end up guessing how a user wants to work ( or you are omniscient). For examples or introductory material that is great and even important for proof of concept if nothing else. To let motivated users exploit the full capabilities of most data sources, however, you need to let them ( or their machines ) interact with existing tools. Further, if you define a machine usable interface (API) you better document your features without having to worry about modal dialogs and button colors. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Sun, 13 Apr 2008 17:23:30 -0700 > From: keithcallenberg at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] Advanced web query interfaces for biological databases > > Thanks for your suggestion, Mike. As a developer I also value the > concept of an open and freely available API, and I wish that more > sites would provide these, but I am not sure it is yet appropriate for > our database as it will be some time before we have a sizable pool of > users, letalone developers. > > Also, I might not be clear on what you mean by "programmatically," but > I think it is a bit short-sighted to limit the scope of web-based > interfaces to only casual queries. I am not usually a supporter of the > term "Web 2.0" because I think it has lately signified little more > than colorful buttons, but I do believe more and more tasks can be > accomplished from within the browser. I believe energy should be put > into moving more advanced tasks online because it removes learning > curves and hardware restrictions, thereby increasing your base of > users. > > I think it is not easy to develop an intuitive web-based UI that is > not fairly restrictive, but that does not mean it should not be > pursued. > > Keith > _________________________________________________________________ Going green? See the top 12 foods to eat organic. http://green.msn.com/galleries/photos/photos.aspx?gid=164&ocid=T003MSN51N1653A From marchywka at hotmail.com Mon Apr 14 17:10:34 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 14 Apr 2008 17:10:34 -0400 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: I almost forgot a couple of examples. I feel compelled to discuss this because I've written so many "awful" scripts to parse variable html. I have encountered few cases where a human readable answer is the only thing you want ( what will you do with most results? Feed them to another program usually.) The example I always mention is eutils, http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html The above link explains that this differs from the web interface and shows a simple API. While investigating a similar problem for SEC filings, I was pointed to more complicated protocols such as SOAP, or various things based on exchange of XML data ( not something I think is suitable for simple tasks, but it is an example with a lot of canned support ). To give you an idea of the parsing problem, I also happened to have made available a script to reverse the above mentioned SEC html here, http://www.spottext.com/marchywka/distroform.cfm?src=bb If you go to the doc page, you will get some idea of what it does and you can download the source code to appreciate the problem ( I couldn't even get bash or PERL to work in reasonable time, I ended up writing C++ code .... ). If you don't have a stable machine interface and just want to write a single GUI, you should go through a check list to make sure this is what you really want. Where does the input come from ( typing is subject to error, even cut/paste can miss a leading or trailing character, etc), do I only produce a single result that can be easily translated into a decision or a manscript with no further effort, etc. For that matter, how will you exhaustively test your interface? Even a GUI should have a way to inject commands from an automated process and have a result another process can verify. Maybe it would help if I knew specifically what you are doing but even visual data (see my molecule viewer at the above link) can be scanned prgammatically. For example, I have an auto resize function to take the non-black area and zoom an image to fill the available space to produce a series of images without user intervention ( you could write a script to scan a bunch of pdb files and write them in some given way without producing a gui, the user can then look at the series of bmp files using existing photo viewers and go back and use the GUI for the few interesting cases ). I almost always expect that the graphical output will be for debugging. You can usually pipe text data into data display programs that know how to display publication quality graphics. This isn't always the case but if it is not, you probably won't find a collection of javascript widgets that are all that useful either. And, in any case, the browser is well accessed with java using code that can be moved with no effort into a stand alone application. Java already supports graphics and there are even existing molecule viewing applets etc that may do much of what you need. But, you can't even really think about portability until you have defined somekind of ( machine-to-machine) interface. >> Date: Sun, 13 Apr 2008 17:23:30 -0700 >> From: keithcallenberg at gmail.com >> To: bbb at bioinformatics.org >> Subject: Re: [BiO BB] Advanced web query interfaces for biological databases >> >> Thanks for your suggestion, Mike. As a developer I also value the >> concept of an open and freely available API, and I wish that more >> sites would provide these, but I am not sure it is yet appropriate for >> our database as it will be some time before we have a sizable pool of >> users, letalone developers. >> >> Also, I might not be clear on what you mean by "programmatically," but >> I think it is a bit short-sighted to limit the scope of web-based >> interfaces to only casual queries. I am not usually a supporter of the >> term "Web 2.0" because I think it has lately signified little more >> than colorful buttons, but I do believe more and more tasks can be >> accomplished from within the browser. I believe energy should be put >> into moving more advanced tasks online because it removes learning >> curves and hardware restrictions, thereby increasing your base of >> users. >> >> I think it is not easy to develop an intuitive web-based UI that is >> not fairly restrictive, but that does not mean it should not be >> pursued. >> >> Keith >> > _________________________________________________________________ > Going green? See the top 12 foods to eat organic. > http://green.msn.com/galleries/photos/photos.aspx?gid=164&ocid=T003MSN51N1653A > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Get in touch in an instant. Get Windows Live Messenger now. http://www.windowslive.com/messenger/overview.html?ocid=TXT_TAGLM_WL_Refresh_getintouch_042008 From jeff at bioinformatics.org Mon Apr 14 21:43:03 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 14 Apr 2008 21:43:03 -0400 Subject: [BiO BB] Course: dChip for Gene Expression and SNP Genotyping Message-ID: <48040827.7050109@bioinformatics.org> Greetings, We're pleased to announce a new course: dChip for Gene Expression and SNP Genotyping; May 19-23, 2008 Join Harvard University Professor Cheng Li in this online workshop on dChip, his software application for Gene Expression and SNP Genotyping analysis. We will cover topics such as importing arrays, performing normalization, model based expression calculations, gene and SNP filtering, clustering, linkage and LOH analysis, and much more. FOR MORE INFORMATION: http://wiki.bioinformatics.org/BI201C_dChip_for_Gene_Expression_and_SNP_Genotyping This course will not be offered on a regular basis, and seats are limited. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From marchywka at hotmail.com Tue Apr 15 10:03:06 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 15 Apr 2008 10:03:06 -0400 Subject: [BiO BB] ...biological databases/ another example- epitope prediction problem In-Reply-To: References: <48041EC5.9070605@umdnj.edu> Message-ID: I think I mentioned this much earlier but let me point to another situation I recently encountered. There are several web sites with epitope prediction servers. The idea is you upload a peptide, select a few parameters, and eventually you get back a list of possible epitopes along with some metrics. So, you may cut/paste a 1-10K sequence and get back hundreds of interesting things and different servers may give different results. What do you expect a typical user to do with this data? In my case, I had a more complicated task as I was looking for incorrectly translated base sequences that could lead to accidental epitope matches with normal proteins. So, I had to use things like fake ribosomes on some edited chromosome sequences, upload the hypothetical translation product to a series of slicer and dicers ( epitope makers ) and then collate all the results, and then do blast or other searches on these peptides. How do you do that with a web interface at every point? Offhand, what is the use case for a web interface on an epitope server that will routinely return 100's of hits with no uniform way to select interesting and uninteresting results? Unfortunately, I had to write scripts to extract data from the html. In many cases, I could use lynx to render the html so I didn't have to parse html source but you can't always rely on this. As html is meant to be interactive, there is rarely a guarantee from the site that it will be stable. A simple API with a text response option would have addressed my needs using results that the site probably had to generate anyway to make the html results. Now, I don't expect ANSI to issue a standard for epitope information exchange, but there are formats ranging from simple text ( my preference ) to XML ( with lots of canned support) that can be easily parsed and remain stable even as user artwork is changed to accomodate fashion fads. You see this everywhere- from the Securities and Exchange Commission to the US patent office. I hadn't realized that the API idea would need to be "sold" but I guess I under estimated how many people think that the graphics are the model- and I think that I recognize the shortage of skilled people in the computer area and the skill set that many professionals in the area possess so I guess I should have known better :) So, if you are still not convinced and the moderator doesn't get annoyed, it may be worthwile to continue this discussion and see if you have more objections that I can't satisfactorily address because I consider it to be an important problem. > From: marchywka at hotmail.com > To: keithcallenberg at gmail.com; bbb at bioinformatics.org > CC: golharam at umdnj.edu > Subject: RE: [BiO BB] Advanced web query interfaces for biological databases > Date: Tue, 15 Apr 2008 08:16:33 -0400 > > > The punchline, repeated below, is that you still need someway to get > your GUI to talk to your data source. > I guess we are just arguing over publication and stability of the interface. > >> Date: Mon, 14 Apr 2008 21:49:54 -0700 >> From: keithcallenberg at gmail.com > _________________________________________________________________ More immediate than e-mail? Get instant access with Windows Live Messenger. http://www.windowslive.com/messenger/overview.html?ocid=TXT_TAGLM_WL_Refresh_instantaccess_042008 From golharam at umdnj.edu Mon Apr 14 23:19:33 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Mon, 14 Apr 2008 23:19:33 -0400 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: Message-ID: <48041EC5.9070605@umdnj.edu> I support this view. "Programmatically" means allowing outside users developing their own software interfacing with your database/website via an API. Although NCBI has a fairly well developed website, there is a lot I can't do from a GUI because of the amount of data we work with. It easier for us to use NCBI's API (E-utilities) to access their live database and extract information in a way we need. Anyone who works with lots of data will know a GUI interface will never be sufficient. Its much easier to accomplish the work with a script or program. Mike Marchywka wrote: >> our database as it will be some time before we have a sizable pool of >> users, letalone developers. > > And what kind of interface will your few developers use? I guess my point is that if you have > a compelling data set, developers will come out of the wood work to support it. > >> Also, I might not be clear on what you mean by "programmatically," but >> I think it is a bit short-sighted to limit the scope of web-based >> interfaces to only casual queries. > > I'm not advocating intentional limitations, just expressing the problem with a GUI. You > end up guessing how a user wants to work ( or you are omniscient). For examples > or introductory material that is great and even important for proof of concept if > nothing else. To let motivated users exploit the full capabilities of most data sources, > however, you need to let them ( or their machines ) interact with existing tools. > > Further, if you define a machine usable interface (API) you better document your features > without having to worry about modal dialogs and button colors. > > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > marchywka at hotmail.com > Note: If I am asking for free stuff, I normally use for hobby/non-profit > information but may use in investment forums, public and private. > Please indicate any concerns if applicable. > Note: Hotmail is possibly blocking my mom's entire > ISP - try me on marchywka at yahoo.com if no reply > here. Thanks. > > >> Date: Sun, 13 Apr 2008 17:23:30 -0700 >> From: keithcallenberg at gmail.com >> To: bbb at bioinformatics.org >> Subject: Re: [BiO BB] Advanced web query interfaces for biological databases >> >> Thanks for your suggestion, Mike. As a developer I also value the >> concept of an open and freely available API, and I wish that more >> sites would provide these, but I am not sure it is yet appropriate for >> our database as it will be some time before we have a sizable pool of >> users, letalone developers. >> >> Also, I might not be clear on what you mean by "programmatically," but >> I think it is a bit short-sighted to limit the scope of web-based >> interfaces to only casual queries. I am not usually a supporter of the >> term "Web 2.0" because I think it has lately signified little more >> than colorful buttons, but I do believe more and more tasks can be >> accomplished from within the browser. I believe energy should be put >> into moving more advanced tasks online because it removes learning >> curves and hardware restrictions, thereby increasing your base of >> users. >> >> I think it is not easy to develop an intuitive web-based UI that is >> not fairly restrictive, but that does not mean it should not be >> pursued. >> >> Keith >> > _________________________________________________________________ > Going green? See the top 12 foods to eat organic. > http://green.msn.com/galleries/photos/photos.aspx?gid=164&ocid=T003MSN51N1653A > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > From hlapp at gmx.net Mon Apr 14 23:40:42 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 14 Apr 2008 23:40:42 -0400 Subject: [BiO BB] Deadline extended for Computational Phyloinformatics Summer Course In-Reply-To: References: Message-ID: Deadline Extension for Computational Phyloinformatics. http://www.nescent.org/courses/2008/comphy/ 24 July - 4 August 2008 In response to requests from our applicants, we are extending the application deadline for our course on Computational Phyloinformatics to Tuesday of next week, April 22. Computational Phyloinformatics is a 10-day summer course sponsored by and held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina (USA) that aims to give students practical knowledge and hands-on skills in phyloinformatics. This course trains students, post-docs, faculty, and researchers in phylogenetic computational thinking: instead of being locked in to using point-and-click off-the-shelf software, we show you how to write your own scripts and programs to customize calculations, implement new statistical analyses, or devise pipelines for high- throughput phylogenetics. Writing and distributing your own Mesquite module, pipelining data through BioPhylo, refining evolutionary models in HyPhy, archiving and querying your lab's productivity in a database, and designing comparative statistical analyses in R: these are not difficult tasks, but there are no textbooks to get you started -- yet the explosion of phyloinformatic data means that the cutting-edge researcher has to be comfortable with computational tools. That's where we come in. This hands-on course gets you over the learning curve: we help you with the installations, show you what libraries to use, and get you comfortable with writing your own programs. The course is divided into three parts: ? Part I: A tutorial review of either Perl, Java, or R (while optional, this part is strongly recommended). ? Part II: Students have the choice of pursuing (1) a Perl track, with focus on BioPerl and Bio::Phylo; (2) a Java track, with focus on how to write a Mesquite module and program workflows that utilize Mesquite modules; or (3) an R track, with a focus on comparative phylogenetic analysis using the libraries Ape, Ouch, and Phylobase. ? Part III: Students choose between (1) a database track (with focus on SQL, BioSQL and database queries of phylogenetic trees); (2) a HyPhy track (with focus on scripting molecular evolution hypothesis tests in a phylogenetic framework); or (3) an advanced R track (with focus on automating analyses using vectorized calculations, advanced plotting and animations, and the R-LaTex document system using Sweave). Students in all tracks will learn how to write basic phylogenetic or comparative analysis scripts, parse NEXUS files, traverse and compute over trees, and make practical use of phylogenetic software libraries. These skills will be learned in a biological context, touching on a diverse array of topics (depending on the track) such as alignment of large numbers of sequences, ancestral state reconstruction, testing for positive selection, etc. INSTRUCTORS James Balhoff, Marguerite Butler, R. Todd Jobe, Hilmar Lapp, Darin London, David Maddison, Spencer Muse, Jeff Oliver, Brian O?Meara, William Piel, Sergei L. Kosakovsky Pond, Ryan Scherle, Todd Vision, Rutger Vos PREREQUISITES Biology: A solid understanding of phylogenetics ? for example, having already taken the Workshop on Molecular Evolution (http:// www.molecularevolution.org/) or equivalent coursework or experience. Computing: Prior experience with Perl, Java, or R; or careful study of the suggested reading materials (see web site). Students should have experience with basic Unix shell commands. All students are expected to bring their own Mac OSX computer (a limited number of loaners are available upon request). FEES Tuition is $600.00. Accommodation is $50/night for a single occupancy apartment, $26/night for double occupancy apartment in housing provided at Duke University (students are also free to make their own housing arrangements). Travel awards of up to $450 each are available to subsidize travel expenses for applicants from underrepresented groups. HOW TO APPLY Apply through the course website (http://www.nescent.org/courses/2008/ comphy). You will be asked to provide a resume, two references, a brief description of your computational and phylogenetic background, and your reasons for taking the course. Course Director: William Piel (piel at treebase.org) Course Administrator: Jory Weintraub (jory at nescent.org) Organizing Committee: Hilmar Lapp, William Piel, Todd Vision, Jory Weintraub From keithcallenberg at gmail.com Tue Apr 15 00:49:54 2008 From: keithcallenberg at gmail.com (Keith Callenberg) Date: Mon, 14 Apr 2008 21:49:54 -0700 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: <48041EC5.9070605@umdnj.edu> References: <48041EC5.9070605@umdnj.edu> Message-ID: I completely agree that there are significant limitations to user interfaces, but there is a reason why at least half of NCBI's users use their web-based tools when they are applicable, and it is that doing so is often simpler and saves time from installing BLAST, ORF Finder, etc on your machine, having to download the data, and making sure you are using the correct command-line options. I do not disagree with your assertion that the half that use the web-based tools are likely doing simpler queries with smaller amounts of data, but this just illustrates that there are tasks that are suitable for a web interface and there are tasks that must be done programmatically. I guess my point of disagreement with Mike is the order or priority in development, because I do not claim that having an API and/or publicly available database is not important. It is just that it would not make sense, at least for our project, to focus on a minority of power users without first accommodating the base of users who are biologists not bioinformaticians. Keith On Mon, Apr 14, 2008 at 8:19 PM, Ryan Golhar wrote: > I support this view. "Programmatically" means allowing outside users > developing their own software interfacing with your database/website via an > API. > > Although NCBI has a fairly well developed website, there is a lot I can't > do from a GUI because of the amount of data we work with. It easier for us > to use NCBI's API (E-utilities) to access their live database and extract > information in a way we need. > > Anyone who works with lots of data will know a GUI interface will never be > sufficient. Its much easier to accomplish the work with a script or > program. > > > Mike Marchywka wrote: > > > > > > > > > > > > our database as it will be some time before we have a sizable pool of > > > users, letalone developers. > > > > > > > And what kind of interface will your few developers use? I guess my point > is that if you have > > a compelling data set, developers will come out of the wood work to > support it. > > > > > > > Also, I might not be clear on what you mean by "programmatically," but > > > I think it is a bit short-sighted to limit the scope of web-based > > > interfaces to only casual queries. > > > > > > > I'm not advocating intentional limitations, just expressing the problem > with a GUI. You > > end up guessing how a user wants to work ( or you are omniscient). For > examples > > or introductory material that is great and even important for proof of > concept if > > nothing else. To let motivated users exploit the full capabilities of most > data sources, > > however, you need to let them ( or their machines ) interact with existing > tools. > > > > Further, if you define a machine usable interface (API) you better > document your features > > without having to worry about modal dialogs and button colors. > > > > > > > > Mike Marchywka > > 586 Saint James Walk > > Marietta GA 30067-7165 > > 404-788-1216 (C)<- leave message > > 989-348-4796 (P)<- emergency only > > marchywka at hotmail.com > > Note: If I am asking for free stuff, I normally use for hobby/non-profit > > information but may use in investment forums, public and private. > > Please indicate any concerns if applicable. > > Note: Hotmail is possibly blocking my mom's entire > > ISP - try me on marchywka at yahoo.com if no reply > > here. Thanks. > > > > > > > > > Date: Sun, 13 Apr 2008 17:23:30 -0700 > > > From: keithcallenberg at gmail.com > > > To: bbb at bioinformatics.org > > > Subject: Re: [BiO BB] Advanced web query interfaces for biological > databases > > > > > > Thanks for your suggestion, Mike. As a developer I also value the > > > concept of an open and freely available API, and I wish that more > > > sites would provide these, but I am not sure it is yet appropriate for > > > our database as it will be some time before we have a sizable pool of > > > users, letalone developers. > > > > > > Also, I might not be clear on what you mean by "programmatically," but > > > I think it is a bit short-sighted to limit the scope of web-based > > > interfaces to only casual queries. I am not usually a supporter of the > > > term "Web 2.0" because I think it has lately signified little more > > > than colorful buttons, but I do believe more and more tasks can be > > > accomplished from within the browser. I believe energy should be put > > > into moving more advanced tasks online because it removes learning > > > curves and hardware restrictions, thereby increasing your base of > > > users. > > > > > > I think it is not easy to develop an intuitive web-based UI that is > > > not fairly restrictive, but that does not mean it should not be > > > pursued. > > > > > > Keith > > > > > > > > _________________________________________________________________ > > Going green? See the top 12 foods to eat organic. > > > http://green.msn.com/galleries/photos/photos.aspx?gid=164&ocid=T003MSN51N1653A > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > From marchywka at hotmail.com Tue Apr 15 08:16:33 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 15 Apr 2008 08:16:33 -0400 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: <48041EC5.9070605@umdnj.edu> Message-ID: The punchline, repeated below, is that you still need someway to get your GUI to talk to your data source. I guess we are just arguing over publication and stability of the interface. > Date: Mon, 14 Apr 2008 21:49:54 -0700 > From: keithcallenberg at gmail.com > > I completely agree that there are significant limitations to user > interfaces, but there is a reason why at least half of NCBI's users > use their web-based tools when they are applicable, and it is that I routinely use pubmed myself, for the reasons stated ( exploratory browsing ) and I am not claiming this is irrelevant. But, they could have implemented it as a simple web form that called their eutils API and achieved both results with little duplicated effort. > doing so is often simpler and saves time from installing BLAST, ORF > Finder, etc on your machine, having to download the data, and making > sure you are using the correct command-line options. Most of this is unrelated as I generally don't download databases ( to save disk space and use the current data and offload look up to a real server). I'm thinking about things like http GET or POST requests that are documented and stable ( but you could think about binary socket protocols if you really want to get extreme) . If you publish these as your site develops, anyone with an immediate need for your data can access it while you still pick colors for your buttons and escape routes from modal dialog boxes. Many local installs still communicate through ports and may or may not use http over their sockets. There is also a trivial but annoying limitation with some GUI-only sites that you can't post a link ( in a forum like this) to a particular result and you need to write a paragraph explaining how to find some simple thing like a particular article or molecule. A simple API based on http GET requests normally lends itself to tractable link creation. > > I guess my point of disagreement with Mike is the order or priority in > development, because I do not claim that having an API and/or publicly > available database is not important. It is just that it would not make > sense, at least for our project, to focus on a minority of power users > without first accommodating the base of users who are biologists not > bioinformaticians. I don't offhand think that biologists are computer illiterate and in any case am not advocating making things unfamiliar to your intended audience. However, even for the computer illiterate, it would probably be a more useful learning curve to learn SQL syntax than navigation of a data-specific GUI unless the latter is incredibly intuitive. And, in the absence of that, I would think that the motivated biologist could find someone who knows SQL. So, I'm just suggesting that a parameterized version of a well known interface like SQL ( with a list of parameters specific to your data ) would not just address power users and may even be more beneficial for your users. And, you still need someway to get your GUI to talk to your data source. I guess we are just arguing over publication and stability of the interface. > > Keith > > On Mon, Apr 14, 2008 at 8:19 PM, Ryan Golhar wrote: >> I support this view. "Programmatically" means allowing outside users >> developing their own software interfacing with your database/website via an >> API. >> >> Although NCBI has a fairly well developed website, there is a lot I can't >> do from a GUI because of the amount of data we work with. It easier for us >> to use NCBI's API (E-utilities) to access their live database and extract >> information in a way we need. >> >> Anyone who works with lots of data will know a GUI interface will never be >> sufficient. Its much easier to accomplish the work with a script or >> program. >> >> >> Mike Marchywka wrote: >> >>> >>> >>> >>> >>>> our database as it will be some time before we have a sizable pool of >>>> users, letalone developers. >>>> >>> >>> And what kind of interface will your few developers use? I guess my point >> is that if you have >>> a compelling data set, developers will come out of the wood work to >> support it. >>> >>> >>>> Also, I might not be clear on what you mean by "programmatically," but >>>> I think it is a bit short-sighted to limit the scope of web-based >>>> interfaces to only casual queries. >>>> >>> >>> I'm not advocating intentional limitations, just expressing the problem >> with a GUI. You >>> end up guessing how a user wants to work ( or you are omniscient). For >> examples >>> or introductory material that is great and even important for proof of >> concept if >>> nothing else. To let motivated users exploit the full capabilities of most >> data sources, >>> however, you need to let them ( or their machines ) interact with existing >> tools. >>> >>> Further, if you define a machine usable interface (API) you better >> document your features >>> without having to worry about modal dialogs and button colors. >>> >>> >>> >>> Mike Marchywka >>> 586 Saint James Walk >>> Marietta GA 30067-7165 >>> 404-788-1216 (C)<- leave message >>> 989-348-4796 (P)<- emergency only >>> marchywka at hotmail.com >>> Note: If I am asking for free stuff, I normally use for hobby/non-profit >>> information but may use in investment forums, public and private. >>> Please indicate any concerns if applicable. >>> Note: Hotmail is possibly blocking my mom's entire >>> ISP - try me on marchywka at yahoo.com if no reply >>> here. Thanks. >>> >>> >>> >>>> Date: Sun, 13 Apr 2008 17:23:30 -0700 >>>> From: keithcallenberg at gmail.com >>>> To: bbb at bioinformatics.org >>>> Subject: Re: [BiO BB] Advanced web query interfaces for biological >> databases >>>> >>>> Thanks for your suggestion, Mike. As a developer I also value the >>>> concept of an open and freely available API, and I wish that more >>>> sites would provide these, but I am not sure it is yet appropriate for >>>> our database as it will be some time before we have a sizable pool of >>>> users, letalone developers. >>>> >>>> Also, I might not be clear on what you mean by "programmatically," but >>>> I think it is a bit short-sighted to limit the scope of web-based >>>> interfaces to only casual queries. I am not usually a supporter of the >>>> term "Web 2.0" because I think it has lately signified little more >>>> than colorful buttons, but I do believe more and more tasks can be >>>> accomplished from within the browser. I believe energy should be put >>>> into moving more advanced tasks online because it removes learning >>>> curves and hardware restrictions, thereby increasing your base of >>>> users. >>>> >>>> I think it is not easy to develop an intuitive web-based UI that is >>>> not fairly restrictive, but that does not mean it should not be >>>> pursued. >>>> >>>> Keith >>>> >>>> >>> _________________________________________________________________ >>> Going green? See the top 12 foods to eat organic. >>> >> http://green.msn.com/galleries/photos/photos.aspx?gid=164&ocid=T003MSN51N1653A >>> >>> _______________________________________________ >>> BBB mailing list >>> BBB at bioinformatics.org >>> http://www.bioinformatics.org/mailman/listinfo/bbb >>> >>> >>> >> >> _________________________________________________________________ Going green? See the top 12 foods to eat organic. http://green.msn.com/galleries/photos/photos.aspx?gid=164&ocid=T003MSN51N1653A From jeff at bioinformatics.org Tue Apr 15 11:24:26 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 15 Apr 2008 11:24:26 -0400 Subject: [BiO BB] Advanced web query interfaces for biological databases In-Reply-To: References: <48041EC5.9070605@umdnj.edu> Message-ID: <4804C8AA.7090402@bioinformatics.org> Hi Mike, Mike Marchywka wrote: > > There is also a trivial but annoying limitation with some GUI-only sites > that you can't post a link ( in a forum like this) to a particular result > and you need to write a paragraph explaining how to find some simple > thing like a particular article or molecule. > A simple API based on http GET requests normally lends itself to tractable link creation. The annoyance may be trivial, but the problem isn't. This is a major problem with "Web 2.0" approaches. And, as a programmer, you're very much limited in your use of GET: multiple step forms (e.g., wizards) and form inputs that accept large datasets (e.g., textarea tags) can't easily be placed/replicated in a single URI. You'll end up needing to store steps and data somewhere. But, if the endpoint is all that matters, simply store the results in a temporary file and link to that. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From marchywka at hotmail.com Tue Apr 15 11:38:58 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 15 Apr 2008 11:38:58 -0400 Subject: [BiO BB] biological database API In-Reply-To: <4804C8AA.7090402@bioinformatics.org> References: <48041EC5.9070605@umdnj.edu> <4804C8AA.7090402@bioinformatics.org> Message-ID: > From: jeff at bioinformatics.org > The annoyance may be trivial, but the problem isn't. This is a major problem with "Web 2.0" approaches. And, as a programmer, you're very much limited in your use of GET: multiple step forms (e.g., wizards) and form inputs that accept large datasets (e.g., textarea tags) can't easily be placed/replicated in a single URI. You'll end up needing to store steps and data somewhere. But, if the endpoint is all that matters, simply store the results in a temporary file and link to that. > Yes, this very much depends on the type of service being provided as a computed result rather than a database lookup doesn't need to be stored on the server. Getting a text or xml response from a POST request fixes most problems and you may be able to describe a POST more easily than navigating a GUI in any case. I would also mention that, having used Coldfusion, it can be hard to generate text from a a server-provided html result in some cases. So, depending on what you are using server side, there could be some effort in extracting the information from the formatting but even with the rather extreme case of CF it is usually only a few more lines of code. > Date: Tue, 15 Apr 2008 11:24:26 -0400 > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] Advanced web query interfaces for biological databases _________________________________________________________________ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008 From hiekeen at gmail.com Wed Apr 16 23:54:27 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Thu, 17 Apr 2008 11:54:27 +0800 Subject: [BiO BB] How to make a network graphic using my genes in pathways? In-Reply-To: <6ec4c2000804030227h515ffca8t52d2d9abad8c89f6@mail.gmail.com> References: <627ca1900804021549t6216fc26u6078146d1ff32229@mail.gmail.com> <6ec4c2000804030227h515ffca8t52d2d9abad8c89f6@mail.gmail.com> Message-ID: thank you very much. How to draw curve line in Cytoscape ? On Thu, Apr 3, 2008 at 5:27 PM, ahmed essaghir wrote: > hi! > you can use Cytoscape www.cytoscape.org > you can create your pathways graph by creating a .sif file (it's easy) > a .sif file is a tab delimited one in which you have three columns : the > first column contains the start nodes id and the second cotains an > abreviation standing for the type of relationship between your nodes (pp for > protein-protein, pr for protein-reaction, ...) and the third column contains > the target nodes id : > example : > let's assume you havz a pathway like this in which a, b, c, d are proteins > ids, so the relationship is "pp" > a ----> b ----> c ---> d > d---> b > then your sif file will be like this > a tabSpace b > b tabSpace c > c tabSpace d > d tabSpace b > > then you can open your graph using cytoscape and if you want to map you > nodes (genes) in the graph you just do "select node from a file" (a file > containing you genes of interest in the same ids of course as you used in > the graph) then you'll have your genes hilighted where ever they are in the > graph. > also you can edit your graph in a user friendly way by deleting and adding > arcs and nodes. > you have also some plugins that allow you to highlight your genes according > to their expression (if you have microarray data expression). > > have fun > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com From marchywka at hotmail.com Sun Apr 20 09:19:54 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Sun, 20 Apr 2008 09:19:54 -0400 Subject: [BiO BB] TopMatch /3D database interface In-Reply-To: <20080402085207.GF9767@came.sbg.ac.at> References: <20080331082118.GF31003@came.sbg.ac.at> <20080402085207.GF9767@came.sbg.ac.at> Message-ID: Hi, Apparently your QCOPS link below is for a structure navigator that requires flash. I guess I'm looking for something like the result here, http://nar.oxfordjournals.org/cgi/reprint/gkm264?ijkey=hqzSJIdl8y6jwUO&keytype=ref ( without even wanting the BLAST results ) but I want a text output to feed to other programs. Can I somehow post a pdb file to your server and get back a (text) list of molecules with similarly shaped and colored ( by atoms that make up the cavity walls ) cavities? This relates to my previous series of posts on the need for an API as opposed to just a human web interface. I may want to use scripts or automated processes to sort through many candidates before using an interactive navigator. I was trying to figure out what databases exist that contain simplified shape and environment information on cavities or surfaces for finding "accidental" ( without any obvious sequence homology) matches or near matches of function. You did mention things like conformations or modifications that distort the shape. Obviously, you would like to find things that are close but not exact and try to figure out what implications these may have for function. Thanks. > Date: Wed, 2 Apr 2008 10:52:07 +0200 > From: markii at came.sbg.ac.at > > Indeed, the structural similarity of dehydrosqualene synthase (PDB codes: 2zco, 2zcp, 2zcq, 2zcr, 2czs) and humane squalene synthase (PDB codes 1ezf) is striking in the view of their low sequence identity. TopMatch-web yields an RMS of 3.5A and a sequence identity of 11% if the respective chains A are compared. > > Talking about finding such similarities: one tool that is really helpful for this task is the qCOPS web service (some advertising again ;-) at > http://navi.services.came.sbg.ac.at/bin/qCOPS.html > For further information on qCOPS, see > Sippl et al. > A Discrete View on Fold Space > Bioinformatics, 24, pp. 870-871 (2008) > (Open Access: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn020?ijkey=7zgnEsdKQIEfrN7&keytype=ref) > > Best regards, > -Markus > > On Die, 01 Apr 2008, Mike Marchywka wrote: >> >> http://www.nature.com/nrd/journal/v7/n4/full/nrd2554.html >> > _________________________________________________________________ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008 From phoebe at deakin.edu.au Sat Apr 26 09:25:32 2008 From: phoebe at deakin.edu.au (Phoebe Chen) Date: Sat, 26 Apr 2008 23:25:32 +1000 Subject: [BiO BB] FIRST CALL FOR PAPERS - APBC 2009 Message-ID: <5.0.1.4.2.20080426231522.04967d80@mail.deakin.edu.au> =============================================================== First Call for Papers - APBC2009 The Seventh Asia-Pacific Bioinformatics Conference (APBC2009) Beijing, China, 13-16 January 2009 http://bioinfo.au.tsinghua.edu.cn/apbc2009/ =============================================================== The Asia Pacific Bioinformatics Conference (APBC) series, founded in 2003, is an annual international forum for exploring research, development and applications of Bioinformatics and Computational Biology. The Seventh Asia-Pacific Bioinformatics Conference, APBC2009 will be held in Beijing, China, following the 2008 Olympic Games. The aim of the conference is to bring together researchers, professionals, and industrial practitioners from all over the world for interaction and exchange of knowledge and ideas in all areas of bioinformatics and computational biology. --------------------------------------------------------------- Important Dates Paper submission open May 1, 2008 Paper submission deadline July 20, 2008 Paper acceptance decision Sep 10, 2008 Camera-ready copy of papers and Author registration Oct 10, 2008 Poster submission open July 20, 2008 Poster submission deadline Sept 20, 2008 Poster acceptance decision Oct 1, 2008 Registration open Sept 20, 2008 Early-bird registration Nov 20, 2008 Conference Jan 13-16, 2009 ---------------------------------------------------------- Confirmed Invited Speakers * (Keynote) David J. Lipman, M.D., Director, NCBI, NLM, NIH, USA * (Keynote) David Botstein, Ph.D., Anthony B. Evnin Professor of Genomics, Director, Lewis Sigler Institute for Integrative Genomics, Princeton University, USA * Martin Vingron, Ph.D., Director at the Max Planck Institute for Molecular Genetics, Head of Computational Molecular Biology Department, Germany * John Mattick, Ph.D., Professor and ARC Federation Fellow at the Institute for Molecular Bioscience, University of Queensland, Australia * Michael B. Eisen, Ph.D., Scientist, Lawrence Berkeley National Lab and Adjunct Assistant Professor, University of California at Berkeley, USA * Pavel Pevzner, Ph.D., Ronald R. Taylow Professor of Computer Science, Director, Center for Algorithmic and Systems Biology at UCSD, USA * Bailin Hao, Ph.D., Professor, Fudan University and Institute of Theoretical Physics, CAS, China * Chunting Zhang, Ph.D., Professor, Tianjin University, China ---------------------------------------------------------- Conference Co-Chairs * Michael Q. Zhang, Cold Spring Harbor Laboratory, USA * Yanda Li, Tsinghua University, China * Xuegong Zhang, Tsinghua University, China -------------------------------------------------------------- Program Committee Co-Chairs * Michael S. Waterman, University of Southern California, USA * Michael Q. Zhang, Cold Spring Harbor Laboratory, USA * Xuegong Zhang, Tsinghua Unviersity, China ---------------------------------------------------------------- Topics of Interest Papers are solicited on, but not limited to, the following topics: * Sequence Analysis * Motif Finding * Recognition of Genes and Functional Elements * RNA Analysis * Physical and Genetic Mapping * Molecular Evolution and Phylogeny * Protein Structure Analysis * Microarray Design and Data Analysis * Deep Sequencing Data Processing * Transcriptome, Gene Expression * Epigenomics * Proteomics and Post-Translational Modifications * Pathways, Networks and Systems * Ontologies * Databases and Data Integration * Biomedical Literature Mining and Understanding * Population Genetics, SNP and Haplotyping * Comparative Genomics ---------------------------------------------------------------- Program Committee Members (Confirmed): * Tatsuya Akutsu,Kyoto University, Japan * Joel Bader, Johns Hopkins University, USA * Harmen Bussemaker, Columbia University, USA * Andrea Califano, Columbia University, USA * Francis Y.L. Chin, Hong Kong University, Hong Kong * Phoebe Chen, Deakin University, Australia * Runsheng Chen, Institute of Biophysics, CAS, China * Xue-wen Chen, University of Kansas, USA * Nadia El-Mabrouk, University of Montreal, Canada * Mikhail Gelfand, Russian Academy of Science, Russia * Roderic Guigo, Centre de Regulacio Genomica, Barcelona, Spain * Jing-Dong Jackie Han, CAS, China * Jenn-Kang Hwang, National Chiao Tung University, Taiwan * Sridhar Hannenhalli, University of Pennsylvania, USA * Daniel Huson, University of T?bingen, Germany * Tao Jiang, University of California Riverside, USA * Uri Keich, Cornell University, USA * Luhua Lai, Peking University, China * Tak Wah Lam, University of Hong Kong, Hong Kong * Charles Lawrence, Brown University, USA * Chris Lee, UCLA, USA * Doheon Lee, KAIST, Korea * Sang Yup Lee, KAIST, Korea * Cheng Li, DFCI/HSPH, USA * Hao Li, UCSF, USA * Jinyan Li, Nanyang Technological University, Singapore * Wen-Hsiung Li, University of Chicago, USA * Wentian Li, Feinstein Institute for Medical Research, USA * Yixue Li, CAS and Shanghai Jiaotong University, China * Jun S. Liu, Harvard University, USA * Jingchu Luo, Peking University, China * Bin Ma, University of Western Ontario, Canada * Hiroshi Mamitsuka, Kyoto University, Japan * Satoru Miyano, University of Tokyo, Japan * Kenta Nakai, University of Tokyo, Japan * Jurg Ott, Rockefeller University, China * Laxmi Parida, IBM Watson Research Center, USA * Pavel A. Pevzner, UCSD, USA * John Quackenbush, Harvard School of Public Health, USA * Mark Ragan, University of Queensland, Australia * Nikolaus Rajewsky, MDC-Berlin, Germany * Ron Shamir, Tel Aviv Univ, Israel * Steven Skiena, State University of New York at Stony Brook, USA * Yun S. Song, UC Berkeley, USA * Paul Spellman, Lawrence Berkeley National Laboratory, USA * Fengzhu Sun, USC, USA * Zhirong Sun, Tsinghua University, China * Masaru Tomita, Keio University, Japan * Martin Vingron, Max Planck Institute for Molecular Genetics, Germany * Lusheng Wang, City University of Hong Kong, Hong Kong * Zhiping Weng, Boston University, USA * Limsoon Wong, National University of Singapore * Wing H. Wong, Stanford University, USA * Eric Xing, Carnegie Mellon University, USA * Ying Xu, University of Georgia, USA * Hong Xue, HKUST, Hong Kong * Ueng Cheng Yang, National Yang Ming University, Taiwan * Weichuan Yu, Hong Kong University of Science and Technology, Hong Kong * Luoxin Zhang, National University of Hong Kong, Hong Kong * Hongyu Zhao, Yale University, USA * Qing Zhou, UCLA, USA -------------------------------------------------------------- Tutorial Co-Chairs * Eric P. Xing, Carnegie Mellon University, USA * Rui Jiang, Tsinghua University, China -------------------------------------------------------------- Organizing Committee * Xuegong Zhang (Chair), Tsinghua University * Luhua Lai, Peking University * Zhirong Sun, Tsinghua University * Jingchu Luo, Peking University * Jingdong Jackie Han, Inst of Genetics & Development, CAS * Shao Li (Poster Co-Chair), Tsinghua University * Rui Jiang, Tsinghua University * Xiaoyan Zhu (Poster Co-Chair), Tsinghua University * Yonglong Zhuang (Publicity Chair), Bioknow Co. -------------------------------------------------------------- APBC Steering Committee * Yi-Ping Phoebe Chen (Chair), Deakin University, Australia * Sang Yup Lee, KAIST, Korea * Satoru Miyano, University of Tokyo, Japan * Mark Ragan, University of Queensland, Australia * Limsoon Wong, National University of Singapore * Michael Q. Zhang, CHSL, USA and Tsinghua University, China ----------------------------------------------------------------- APBC2009 invites high-quality original papers and posters on any topic related to Bioinformatics and Computational Biology. Accepted papers will be invited to be published in the journal BMC Bioinformatics. The conference will be held at Tsinghua University three months after the Beijing 2008 Olympic Games and two weeks before the traditional Chinese New Year. Post-conference tours will be arranged to major scenery and historical cities in Northern and Southern China. ------------------------------------------------------------------- Call for Papers APBC2009 invites high-quality original full papers on any topic related to Bioinformatics and Computational Biology. The submitted papers must have not been published or under the consideration for publication in any other journals or conferences with formal proceedings. All accepted papers will be arranged for oral presentation at the conference. Accepted papers will be invited to be published in the journal BMC Bioinformatics, following the journal?s publication policy. Papers should not be more than 10 pages in length, including the title, authors and addresses, abstract, text, figures and tables, and references. The manuscripts can be prepared with any of the popular word-processing tools but should be submitted as PDF files. The main text font should not be single-column, single-spaced, with fonts not smaller than 10pt. Tables and figures should be placed among the texts. Color figures are allowed at submission. Authors can provide supplementary materials at their own website if necessary, and can submitted as an attachment when their papers are accepted to be included on the journals. The online submission system will be open from May 1 to July 20, 2008. ---------------------------------------------------------------