From bioinformaticsckk at yahoo.co.in Thu Nov 1 04:52:33 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Thu, 1 Nov 2001 09:52:33 +0000 (GMT) Subject: [BiO BB] to ingrid Message-ID: <20011101095233.8089.qmail@web8005.mail.in.yahoo.com> Hi Ingrid, one more book called sequence analysis primer written by Gribskov is a good one for beginner interested in sequence analysis. Good luck, kiran kumar ____________________________________________________________ Do You Yahoo!? For regular News updates go to http://in.news.yahoo.com From davidow at molbio.mgh.harvard.edu Thu Nov 1 12:53:17 2001 From: davidow at molbio.mgh.harvard.edu (Lance Davidow 617.726-5955) Date: Thu, 01 Nov 2001 12:53:17 -0500 (EST) Subject: [BiO BB] Blast In-Reply-To: <877B003B6F03D511A22E00B0D078E7A85428FA@hst.satyam.com> References: <877B003B6F03D511A22E00B0D078E7A85428FA@hst.satyam.com> Message-ID: <1004637197.3be18c0d2c408@molbio.mgh.harvard.edu> Sam, The NCBI gives out the rules and some examples using lynx for how to automate submissions to QBlast. They recommend that your script wait for the answer to come back from the previous query before firing off the next one. I have used PERL to automate large numbers of blasts using their directions. Please see their http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html Cheers, Lance Quoting Sameer_Mohta : > Hi All, > > can we schedule a batch BLAST job on NCBI server. > I mean i want to run BLAST for 100 sequences. But i don't want to do it > manually. i want to submit all these sequences in a single shot. is > there > any facility available ? > > sam > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > Lance Davidow, PhD Director of Bioinformatics Dept of Molecular Biology, Wellman 901 Massachusetts General Hospital Boston, MA 02114 617.726-5955 davidow at molbio.mgh.harvard.edu From jeff at bioinformatics.org Thu Nov 1 17:44:39 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 01 Nov 2001 17:44:39 -0500 Subject: [BiO BB] Talk in Cambridge, MA: Applications, Design, and Development of Biochips Message-ID: <3BE1D057.A16552C9@bioinformatics.org> Abstract: Control Systems and SSCS Joint Meeting - 6:00PM, Wednesday 16 January 2002 Title: Applications, Design, and Development of Biochips Speaker: Manish Deshpande, Coventor, Inc. The tremendous impact that biotechnology will have on modern society is just now beginning to be felt. One of the driving forces in the field of biotechnology is the increasing availability of ever more powerful diagnostic and analytic techniques and information processing tools, which have allowed such feats as the decoding of the human genome. In recent years, many biochemical processing and analysis operations have benefited by the development of microscale biochemical devices. Often called "biochips," these microscale devices hold the promise of reduced analysis cost and time, while simultaneously improving the quality of resulting information. Applications of biochips include such diverse areas as DNA and protein diagnostics, high throughput drug screening, and detection of biological and chemical warfare agents. The embodiment of biochips can encompass many forms, ranging from simple plastic devices to complex silicon-based MEMS structures that incorporate microscale mechanical moving parts, electronic circuits, and on-chip biochemical detection and processing. This presentation will describe the different applications of biochips and will contrast the performance of these microscale systems with more conventional approaches. In addition to describing many of the applications of biochips, this discussion will focus on aspects of their design and development. Issues such as materials compatibility, integration of electronics and optics with biochemical processing systems, applications of MEMS in biotechnology, and fabrication issues associated with biochips will be discussed. Due to the inherent interdisciplinary nature of the development of biochips, design methodologies and design tools have been developed to facilitate interdisciplinary biochip development efforts. The appropriate role and use of such methods and tools will be examined in the context of industrial and academic examples of biochip development efforts. Speaker Biography: Dr. Manish Deshpande is the Manager of the Biotechnology and Microfluidics group at Coventor, Inc, in Cambridge (www.coventor.com). Coventor provides software design tools and design services for MEMS and microscale biotechnology and fluidics product development. Dr. Deshpande joined Coventor (formerly Microcosm Technologies) in 1996 after completing his Ph.D. and post doctoral studies in Mechanical Engineering at Penn State University. His research at Penn State University primarily involved work in the field of computational fluid dynamics and its application to a wide range of problems including cavitation, combustion and multiphase flow. Dr. Deshpande is currently managing numerous biochip design and fabrication projects at Coventor and has a unique understanding of the issues that are confronting biochip technology development. Location and Directions: The Boston Chapter of the IEEE Control Systems Society and SSCS along with the ACM will meet at 6:00PM on 16 January 2002 at the U.S. Dept. of Transportation, Volpe National Transportation Systems Center, 55 Broadway St., Cambridge, MA. Parking is generally available on the small street behind the Volpe Center (check with the guard inside if you need assistance). The small parking lot in front of the Volpe Center is closed to the meeting (closes at 6:00PM). Complete directions to the Volpe Center (just a one block walk through the Marriott hotel from the Kendall Square Redline exit) can be viewed at their website at: http://www.volpe.dot.gov/about/visiting.html Due to heightened security everyone will have to enter the building through the side door, and there will be plenty of signs directing you to it. Light refreshments will be available at 6:00PM; the talk will begin at 6:15PM. Optional (you pay) dinner with the speaker may follow at a restaurant nearby. For more info contact either George Anagnostopoulos (Anagnostopoulos at volpe.dot.gov) or Allan Kleinman (akleinman at drc.com) or Bruce Hecht (bruce.hecht at analog.com). CENTERFOLD SUMMARY: ------------------ Control Systems and SSCS --WEDNESDAY, 16 January 2002 Applications, Design, and Development of Biochips Manish Deshpande, Coventor, Inc. This presentation will describe the many applications of biochips in such areas as DNA and protein diagnostics, high throughput drug screening and detection of biological and chemical warfare agents. Aspects of biochip design such as issues of material compatibility, integration of electronics and optics with biochemical processing systems, applications of MEMS in biotechnology and biochip fabrication issues will be discussed. Examples will be provided of the interdisciplinary nature of the development of biochips, design methodologies and design tools in both the industrial and academic setting. Meeting at 6:00PM in the Volpe NTSC/DOT in Cambridge. An optional dinner with the speaker may follow at a nearby restaurant. For further information contact George Anagnostopoulos (Anagnostopoulos at volpe.dot.gov) or Allan Kleinman (akleinman at drc.com) or Bruce Hecht (bruce.hecht at analog.com). From bioinfo_india at yahoo.com Fri Nov 2 03:57:17 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Fri, 2 Nov 2001 00:57:17 -0800 (PST) Subject: [BiO BB] to ingrid In-Reply-To: <20011101095233.8089.qmail@web8005.mail.in.yahoo.com> Message-ID: <20011102085717.37809.qmail@web14509.mail.yahoo.com> Sequence analysis primer is quite old book. however concepts are well explained and can be refereed to as fundamentals of this area. Further to this, there are many areas in bioinformatics to be covered for example genome analysis , protein domain architechture analysis and phylogenetics these all need to be emphasized. considering all this Braxevanis and David mount books are better. but remember all these books are assorted journal club papers. these books are equivelnt to collection of journals in your rack. --- kiran challapalli wrote: > Hi Ingrid, > one more book called sequence analysis primer > written > by Gribskov is a good one for beginner interested in > sequence analysis. > Good luck, > kiran kumar > > ____________________________________________________________ > Do You Yahoo!? > For regular News updates go to > http://in.news.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com From idoerg at cc.huji.ac.il Fri Nov 2 04:23:56 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Fri, 2 Nov 2001 11:23:56 +0200 (GMT+0200) Subject: [BiO BB] to ingrid In-Reply-To: <20011102085717.37809.qmail@web14509.mail.yahoo.com> Message-ID: Speaking of edited collections, Methods in Enzymology vols. 183 and 266 are good introductory texts. 266 is more up-to-date. Iddo On Fri, 2 Nov 2001, Peri Suraj wrote: : but remember all these books are assorted journal : club papers. these books are equivelnt to collection : of journals in your rack. : : --- kiran challapalli : wrote: : > Hi Ingrid, : > one more book called sequence analysis primer : > written : > by Gribskov is a good one for beginner interested in : > sequence analysis. : > Good luck, : > kiran kumar : > : > : ____________________________________________________________ : > Do You Yahoo!? : > For regular News updates go to : > http://in.news.yahoo.com : > : > _______________________________________________ : > BiO_Bulletin_Board maillist- : > BiO_Bulletin_Board at bioinformatics.org : > : http://bioinformatics.org/mailman/listinfo/bio_bulletin_board : > : : : ===== : PIL/CEBI/SDU/DK : : __________________________________________________ : Do You Yahoo!? : Find a job, post your resume. : http://careers.yahoo.com : : _______________________________________________ : BiO_Bulletin_Board maillist- BiO_Bulletin_Board at bioinformatics.org : http://bioinformatics.org/mailman/listinfo/bio_bulletin_board : : -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From kiran_ayyagari at yahoo.com Fri Nov 2 04:40:06 2001 From: kiran_ayyagari at yahoo.com (Ayyagari Kiran) Date: Fri, 2 Nov 2001 01:40:06 -0800 (PST) Subject: [BiO BB] Demo projects in pharmacogenomics In-Reply-To: <200111011700.MAA19085@www.bioinformatics.org> Message-ID: <20011102094006.67241.qmail@web11906.mail.yahoo.com> Hi! all, Kindly suggest me a demo project in the area of pharmacogenomics.And Kindly enlist the steps to do it. I have the necessary software packages to do the same. Thanks in advance. -Kiran __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com From RMayreddy at NBME.org Fri Nov 2 11:46:30 2001 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Fri, 2 Nov 2001 11:46:30 -0500 Subject: [BiO BB] Demo projects in pharmacogenomics Message-ID: WE are planning to set up a training class on pharmacogenomics. Can you, especially Kiran, suggest software, and other relavent info. Thanks, Ravi -----Original Message----- From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] Sent: Friday, November 02, 2001 4:40 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Demo projects in pharmacogenomics Hi! all, Kindly suggest me a demo project in the area of pharmacogenomics.And Kindly enlist the steps to do it. I have the necessary software packages to do the same. Thanks in advance. -Kiran __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From bioinfo_india at yahoo.com Fri Nov 2 12:13:37 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Fri, 2 Nov 2001 09:13:37 -0800 (PST) Subject: [BiO BB] Demo projects in pharmacogenomics In-Reply-To: Message-ID: <20011102171337.26015.qmail@web14508.mail.yahoo.com> hi, where is this training class comingup. is this somewhere in US or in india. if you are planing to make this training in a bigway please post abt it in detail. cheers s --- Ravi Mayreddy wrote: > WE are planning to set up a training class on > pharmacogenomics. Can you, > especially Kiran, suggest software, and other > relavent info. > > Thanks, > Ravi > > -----Original Message----- > From: Ayyagari Kiran > [mailto:kiran_ayyagari at yahoo.com] > Sent: Friday, November 02, 2001 4:40 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Demo projects in pharmacogenomics > > > Hi! all, > > Kindly suggest me a demo project in the area of > pharmacogenomics.And Kindly enlist the steps to do > it. > > I have the necessary software packages to do the > same. > Thanks in advance. > > -Kiran > > > > > > > __________________________________________________ > Do You Yahoo!? > Find a job, post your resume. > http://careers.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com From RMayreddy at NBME.org Fri Nov 2 12:43:28 2001 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Fri, 2 Nov 2001 12:43:28 -0500 Subject: [BiO BB] Demo projects in pharmacogenomics Message-ID: It will be in Philadelphia, USA -Ravi -----Original Message----- From: Peri Suraj [mailto:bioinfo_india at yahoo.com] Sent: Friday, November 02, 2001 12:14 PM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] Demo projects in pharmacogenomics hi, where is this training class comingup. is this somewhere in US or in india. if you are planing to make this training in a bigway please post abt it in detail. cheers s --- Ravi Mayreddy wrote: > WE are planning to set up a training class on > pharmacogenomics. Can you, > especially Kiran, suggest software, and other > relavent info. > > Thanks, > Ravi > > -----Original Message----- > From: Ayyagari Kiran > [mailto:kiran_ayyagari at yahoo.com] > Sent: Friday, November 02, 2001 4:40 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Demo projects in pharmacogenomics > > > Hi! all, > > Kindly suggest me a demo project in the area of > pharmacogenomics.And Kindly enlist the steps to do > it. > > I have the necessary software packages to do the > same. > Thanks in advance. > > -Kiran > > > > > > > __________________________________________________ > Do You Yahoo!? > Find a job, post your resume. > http://careers.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From cupton at uvic.ca Fri Nov 2 13:28:36 2001 From: cupton at uvic.ca (Chris Upton) Date: Fri, 2 Nov 2001 10:28:36 -0800 Subject: [BiO BB] Re: Blast In-Reply-To: <200111021700.MAA04807@www.bioinformatics.org> References: <200111021700.MAA04807@www.bioinformatics.org> Message-ID: We've created perl scripts to submit large numbers of blast searches and also look for new hit in the output. See BSU and BSO at http://athena.bioc.uvic.ca/genomes/ -- Chris Upton PhD Associate Professor Biochemistry and Microbiology Phone 250-721-6507 University of Victoria PO Box 3055 Victoria Fax 250-721-8855 BC V8W 3P6, Canada http://web.uvic.ca/~cupton From guoqing_lu at yahoo.ca Fri Nov 2 15:44:55 2001 From: guoqing_lu at yahoo.ca (guoqing lu) Date: Fri, 2 Nov 2001 12:44:55 -0800 (PST) Subject: [BiO BB] cDNA annotation Message-ID: <20011102204455.72757.qmail@web14805.mail.yahoo.com> Dear group, We have a big dataset from microarray experiments and want to have them annotated. Annotation is expected to be done following these steps: 1. Data pre-processing ( mask repeats and cloning vector fragments). 2. Database searches ( to examine whether the sequence has a known protein, whether it has been localized, and whether there is a possibility of forming a contig). 3. EST clustering (initial clustering: performed based on a measure of high sequence identity; assembly; alignment processing: get rid of errors and alternate forms of expressed sequences; Cluster joining) 4. Finding an ORF 5. Find global homologies and align with sequence 6. Location and transmembrane segments 7. Motifs prediction 8. Structure prediction Could you please give some comments? And does anybody know any automatic annotation tools available online or for download? I appreciate your help! Gabriel __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com From Sameer_Mohta at satyam.com Sun Nov 4 05:12:16 2001 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Sun, 4 Nov 2001 15:42:16 +0530 Subject: [BiO BB] primer Message-ID: <877B003B6F03D511A22E00B0D078E7A8542913@hst.satyam.com> Hi Can we install Primer3 software on Windows. From documentation of Primer3 i got the flavour that Primer3 is available for Linux and Unix. sam From jkwaran at rediffmail.com Mon Nov 5 07:05:55 2001 From: jkwaran at rediffmail.com (j kamesh) Date: 5 Nov 2001 12:05:55 -0000 Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics Message-ID: <20011105120555.28297.qmail@mailFA5.rediffmail.com> Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in biosciences then my MCA, i have 3 yrs in IT now im looking for some opportinuties in bioinformatics.pls help me so that i can join as some trainy or some thing.suggest me some sites for free tutorials on bioinformatics tools. some e books, news letters sites. -Regs j.kamesh On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > WE are planning to set up a training class on > pharmacogenomics. Can you, > especially Kiran, suggest software, and other relavent > info. > > Thanks, > Ravi > > -----Original Message----- > From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > Sent: Friday, November 02, 2001 4:40 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Demo projects in pharmacogenomics > > > Hi! all, > > Kindly suggest me a demo project in the area of > pharmacogenomics.And Kindly enlist the steps to do it. > > I have the necessary software packages to do the same. > Thanks in advance. > > -Kiran > > > > > > > __________________________________________________ > Do You Yahoo!? > Find a job, post your resume. > http://careers.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > From gladium at terra.com.br Mon Nov 5 09:25:37 2001 From: gladium at terra.com.br (Marcos Oliveira de Carvalho) Date: Mon, 5 Nov 2001 12:25:37 -0200 Subject: [BiO BB] Demo projects in pharmacogenomics References: <20011105120555.28297.qmail@mailFA5.rediffmail.com> Message-ID: <001101c16605$c60e9a80$2ea4b0c8@virion> Hi Kamesh Take a look: http://linkage.rockefeller.edu/wli/bioinfocourse/ http://www.math.tau.ac.il/~rshamir/algmb/algmb98.html http://www.sequenceanalysis.com/ http://www.agr.kuleuven.ac.be/vakken/i287/bioinformatica.htm http://www.hgmp.mrc.ac.uk/CCP11/ http://www.uni-mainz.de/~cfrosch/bc4s/example.html http://www.cse.ucsc.edu/classes/cmpe177/ http://bioinfo.mbb.yale.edu/mbb447b-99/ http://www.cse.ucsc.edu/classes/cmp243/ Best regards Marcos de Carvalho ----- Original Message ----- From: "j kamesh" To: Sent: Monday, November 05, 2001 10:05 AM Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in biosciences then my MCA, i have 3 yrs in IT now im looking for some opportinuties in bioinformatics.pls help me so that i can join as some trainy or some thing.suggest me some sites for free tutorials on bioinformatics tools. some e books, news letters sites. > -Regs > j.kamesh > > On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > > WE are planning to set up a training class on > > pharmacogenomics. Can you, > > especially Kiran, suggest software, and other relavent > > info. > > > > Thanks, > > Ravi > > > > -----Original Message----- > > From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > > Sent: Friday, November 02, 2001 4:40 AM > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] Demo projects in pharmacogenomics > > > > > > Hi! all, > > > > Kindly suggest me a demo project in the area of > > pharmacogenomics.And Kindly enlist the steps to do it. > > > > I have the necessary software packages to do the same. > > Thanks in advance. > > > > -Kiran > > > > > > > > > > > > > > __________________________________________________ > > Do You Yahoo!? > > Find a job, post your resume. > > http://careers.yahoo.com > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > board > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > board > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From RMayreddy at NBME.org Mon Nov 5 09:23:49 2001 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Mon, 5 Nov 2001 09:23:49 -0500 Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics Message-ID: Where are you located? -ravi -----Original Message----- From: j kamesh [mailto:jkwaran at rediffmail.com] Sent: Monday, November 05, 2001 7:06 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in biosciences then my MCA, i have 3 yrs in IT now im looking for some opportinuties in bioinformatics.pls help me so that i can join as some trainy or some thing.suggest me some sites for free tutorials on bioinformatics tools. some e books, news letters sites. -Regs j.kamesh On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > WE are planning to set up a training class on > pharmacogenomics. Can you, > especially Kiran, suggest software, and other relavent > info. > > Thanks, > Ravi > > -----Original Message----- > From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > Sent: Friday, November 02, 2001 4:40 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Demo projects in pharmacogenomics > > > Hi! all, > > Kindly suggest me a demo project in the area of > pharmacogenomics.And Kindly enlist the steps to do it. > > I have the necessary software packages to do the same. > Thanks in advance. > > -Kiran > > > > > > > __________________________________________________ > Do You Yahoo!? > Find a job, post your resume. > http://careers.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board > _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Louis at exxcalibur.net Mon Nov 5 14:58:10 2001 From: Louis at exxcalibur.net (Louis Pilli) Date: Mon, 05 Nov 2001 14:58:10 -0500 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #126 - 3 msgs In-Reply-To: <200111051700.MAA22601@www.bioinformatics.org> Message-ID: on 11/5/01 12:00 PM, bio_bulletin_board-admin at bioinformatics.org at bio_bulletin_board-admin at bioinformatics.org wrote: > > Send BiO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of BiO_Bulletin_Board digest...") > > > Today's Topics: > > 1. Re: RE: [BiO BB] Demo projects in pharmacogenomics (j kamesh) > 2. RE: Demo projects in pharmacogenomics (Marcos Oliveira de Carvalho) > 3. RE: Re: RE: [BiO BB] Demo projects in pharmacogenomics (Ravi Mayreddy) > > --__--__-- > > Message: 1 > Date: 5 Nov 2001 12:05:55 -0000 > From: "j kamesh" > Reply-To: "j kamesh" > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > charset=iso-8859-1 > Reply-To: bio_bulletin_board at bioinformatics.org > > > Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > biosciences then my MCA, i have 3 yrs in IT now im looking for some > opportinuties in bioinformatics.pls help me so that i can join as some trainy > or some thing.suggest me some sites for free tutorials on bioinformatics > tools. some e books, news letters sites. > -Regs > j.kamesh > > On Fri, 02 Nov 2001 Ravi Mayreddy wrote : >> WE are planning to set up a training class on >> pharmacogenomics. Can you, >> especially Kiran, suggest software, and other relavent >> info. >> >> Thanks, >> Ravi >> >> -----Original Message----- >> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] >> Sent: Friday, November 02, 2001 4:40 AM >> To: bio_bulletin_board at bioinformatics.org >> Subject: [BiO BB] Demo projects in pharmacogenomics >> >> >> Hi! all, >> >> Kindly suggest me a demo project in the area of >> pharmacogenomics.And Kindly enlist the steps to do it. >> >> I have the necessary software packages to do the same. >> Thanks in advance. >> >> -Kiran >> >> >> >> >> >> >> __________________________________________________ >> Do You Yahoo!? >> Find a job, post your resume. >> http://careers.yahoo.com >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - >> BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- >> board >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - >> BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- >> board >> > > > > --__--__-- > > Message: 2 > From: "Marcos Oliveira de Carvalho" > To: > Subject: RE: [BiO BB] Demo projects in pharmacogenomics > Date: Mon, 5 Nov 2001 12:25:37 -0200 > charset="iso-8859-1" > Reply-To: bio_bulletin_board at bioinformatics.org > > Hi Kamesh > > Take a look: > http://linkage.rockefeller.edu/wli/bioinfocourse/ > http://www.math.tau.ac.il/~rshamir/algmb/algmb98.html > http://www.sequenceanalysis.com/ > http://www.agr.kuleuven.ac.be/vakken/i287/bioinformatica.htm > http://www.hgmp.mrc.ac.uk/CCP11/ > http://www.uni-mainz.de/~cfrosch/bc4s/example.html > http://www.cse.ucsc.edu/classes/cmpe177/ > http://bioinfo.mbb.yale.edu/mbb447b-99/ > http://www.cse.ucsc.edu/classes/cmp243/ > > Best regards > Marcos de Carvalho > > > > ----- Original Message ----- > From: "j kamesh" > To: > Sent: Monday, November 05, 2001 10:05 AM > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > >> >> Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > biosciences then my MCA, i have 3 yrs in IT now im looking for some > opportinuties in bioinformatics.pls help me so that i can join as some > trainy or some thing.suggest me some sites for free tutorials on > bioinformatics tools. some e books, news letters sites. >> -Regs >> j.kamesh >> >> On Fri, 02 Nov 2001 Ravi Mayreddy wrote : >>> WE are planning to set up a training class on >>> pharmacogenomics. Can you, >>> especially Kiran, suggest software, and other relavent >>> info. >>> >>> Thanks, >>> Ravi >>> >>> -----Original Message----- >>> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] >>> Sent: Friday, November 02, 2001 4:40 AM >>> To: bio_bulletin_board at bioinformatics.org >>> Subject: [BiO BB] Demo projects in pharmacogenomics >>> >>> >>> Hi! all, >>> >>> Kindly suggest me a demo project in the area of >>> pharmacogenomics.And Kindly enlist the steps to do it. >>> >>> I have the necessary software packages to do the same. >>> Thanks in advance. >>> >>> -Kiran >>> >>> >>> >>> >>> >>> >>> __________________________________________________ >>> Do You Yahoo!? >>> Find a job, post your resume. >>> http://careers.yahoo.com >>> >>> _______________________________________________ >>> BiO_Bulletin_Board maillist - >>> BiO_Bulletin_Board at bioinformatics.org >>> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- >>> board >>> >>> _______________________________________________ >>> BiO_Bulletin_Board maillist - >>> BiO_Bulletin_Board at bioinformatics.org >>> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- >>> board >>> >> >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > > --__--__-- > > Message: 3 > From: Ravi Mayreddy > To: "'bio_bulletin_board at bioinformatics.org'" > > Subject: RE: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > Date: Mon, 5 Nov 2001 09:23:49 -0500 > charset="iso-8859-1" > Reply-To: bio_bulletin_board at bioinformatics.org > > Where are you located? > > -ravi > > -----Original Message----- > From: j kamesh [mailto:jkwaran at rediffmail.com] > Sent: Monday, November 05, 2001 7:06 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > > > Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > biosciences then my MCA, i have 3 yrs in IT now im looking for some > opportinuties in bioinformatics.pls help me so that i can join as some > trainy or some thing.suggest me some sites for free tutorials on > bioinformatics tools. some e books, news letters sites. > -Regs > j.kamesh > > On Fri, 02 Nov 2001 Ravi Mayreddy wrote : >> WE are planning to set up a training class on >> pharmacogenomics. Can you, >> especially Kiran, suggest software, and other relavent >> info. >> >> Thanks, >> Ravi >> >> -----Original Message----- >> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] >> Sent: Friday, November 02, 2001 4:40 AM >> To: bio_bulletin_board at bioinformatics.org >> Subject: [BiO BB] Demo projects in pharmacogenomics >> >> >> Hi! all, >> >> Kindly suggest me a demo project in the area of >> pharmacogenomics.And Kindly enlist the steps to do it. >> >> I have the necessary software packages to do the same. >> Thanks in advance. >> >> -Kiran >> >> >> >> >> >> >> __________________________________________________ >> Do You Yahoo!? >> Find a job, post your resume. >> http://careers.yahoo.com >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - >> BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- >> board >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - >> BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- >> board >> > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > --__--__---- > > End of BiO_Bulletin_Board Digest Biotech and Pharma opportunities in Canada! Visit http://www.exxcalibur.net and register with us. From tvavouri at hotmail.com Tue Nov 6 08:56:47 2001 From: tvavouri at hotmail.com (Tanya Vavouri) Date: Tue, 06 Nov 2001 13:56:47 +0000 Subject: [BiO BB] Good OOP and Java Book Message-ID: Hi, I am starting a bioinformatics project in which I'll develop a program in Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am looking for a good book that will introduce me to OOP and then teach me Java. Are there any books that you would recommend ? I have found some titles but I'd like to have some opinions as well. Thanks in advance, Tanya _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From john_scheiderer at msn.com Tue Nov 6 09:37:44 2001 From: john_scheiderer at msn.com (John Scheiderer) Date: Tue, 6 Nov 2001 09:37:44 -0500 Subject: [BiO BB] Good OOP and Java Book Message-ID: Just Java 2 by Peter Van Der Linden is an excellent book to learn Java (and does cover some OOP). http://www.amazon.com/exec/obidos/ASIN/0130105341/qid=1005057200/sr=8-1/ref=sr_8_7_1/104-7110682-2029545 ----- Original Message ----- From: Tanya Vavouri Sent: Tuesday, November 06, 2001 9:13 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Good OOP and Java Book Hi, I am starting a bioinformatics project in which I'll develop a program in Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am looking for a good book that will introduce me to OOP and then teach me Java. Are there any books that you would recommend ? I have found some titles but I'd like to have some opinions as well. Thanks in advance, Tanya _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_boardGet more from the Web. FREE MSN Explorer download : http://explorer.msn.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Kyle.Klicker at pnl.gov Tue Nov 6 12:02:36 2001 From: Kyle.Klicker at pnl.gov (Klicker, Kyle R) Date: Tue, 06 Nov 2001 09:02:36 -0800 Subject: [BiO BB] Good OOP and Java Book Message-ID: <202822BFB70EBC4BB3EAFD853EE2B6BF405DDB@pnlmse10.pnl.gov> Personally, I like the Deitel and Deitel books, but that's just me. They cover OOP well I think. Hope this helps, Kyle -----Original Message----- From: Tanya Vavouri [mailto:tvavouri at hotmail.com] Sent: Tuesday, November 06, 2001 5:57 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Good OOP and Java Book Hi, I am starting a bioinformatics project in which I'll develop a program in Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am looking for a good book that will introduce me to OOP and then teach me Java. Are there any books that you would recommend ? I have found some titles but I'd like to have some opinions as well. Thanks in advance, Tanya _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From stein at fieldmuseum.org Tue Nov 6 12:09:46 2001 From: stein at fieldmuseum.org (Jennifer Steinbachs) Date: Tue, 6 Nov 2001 11:09:46 -0600 (CST) Subject: [BiO BB] Good OOP and Java Book In-Reply-To: <202822BFB70EBC4BB3EAFD853EE2B6BF405DDB@pnlmse10.pnl.gov> Message-ID: For OOP, I was encouraged to read: G. Booch. Object-oriented analysis and design with applications. I have the 2nd edition (ISBN 0905353402) but there is probably a newer version out by now. -jennifer On Tue, 6 Nov 2001, Klicker, Kyle R wrote: >Personally, I like the Deitel and Deitel books, but that's just me. They cover >OOP well I think. > >Hope this helps, > >Kyle > >-----Original Message----- >From: Tanya Vavouri [mailto:tvavouri at hotmail.com] >Sent: Tuesday, November 06, 2001 5:57 AM >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Good OOP and Java Book > > >Hi, > >I am starting a bioinformatics project in which I'll develop a program in >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am >looking for a good book that will introduce me to OOP and then teach me >Java. Are there any books that you would recommend ? I have found some >titles but I'd like to have some opinions as well. > >Thanks in advance, >Tanya > > >_________________________________________________________________ >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist http://compbiology.org ----------------------------------- From bioinfo_india at yahoo.com Tue Nov 6 12:37:46 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Tue, 6 Nov 2001 09:37:46 -0800 (PST) Subject: [BiO BB] Unix or Linux In-Reply-To: Message-ID: <20011106173747.84595.qmail@web14506.mail.yahoo.com> Hi group, I am on a survey and also to know what is the type of computing environment, big and famous labs in bioinformatics prefer. Which server ( A unix or Linux) you prefer,that has all the important databases for critical research purpose, considering robustness of the system. 1. UNIX ( Digital, Solaris, IRIX that are proprietory and robust) 2. LINUX( Free, widely used and flexible) Folks, what would you prefer? Please post your suggestion and views ! cheers sp ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com From Joel.Dudley at DevelopOnline.com Tue Nov 6 17:10:02 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Tue, 6 Nov 2001 15:10:02 -0700 Subject: [BiO BB] Unix or Linux Message-ID: well linux of course!! all NCBI libraries are available for linux. Also, most major databases like MySQL and oracel will run on it. -----Original Message----- From: Peri Suraj [mailto:bioinfo_india at yahoo.com] Sent: Tuesday, November 06, 2001 10:38 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Unix or Linux Hi group, I am on a survey and also to know what is the type of computing environment, big and famous labs in bioinformatics prefer. Which server ( A unix or Linux) you prefer,that has all the important databases for critical research purpose, considering robustness of the system. 1. UNIX ( Digital, Solaris, IRIX that are proprietory and robust) 2. LINUX( Free, widely used and flexible) Folks, what would you prefer? Please post your suggestion and views ! cheers sp ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From sharma_animesh at hotmail.com Wed Nov 7 09:00:53 2001 From: sharma_animesh at hotmail.com (Animesh Sharma) Date: Wed, 07 Nov 2001 09:00:53 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #127 - 3 msgs Message-ID: hello to all the members of bulletin board, i just joined this community and i feel it is a good place to share views and tools :) . i m a student of bioinformatics in JNU, delhi and wud like to have some help on a good book on ALGORITHM used in bioinformatics like SmithWaterman , Chous-Fasmann etc... or any links which explain this . thanks alot in advance ani ********************************************************************** the answer lies in genome ********************************************************************** dr.animesh sharma bioinformatics centre JNU,Delhi >From: bio_bulletin_board-admin at bioinformatics.org >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: BiO_Bulletin_Board digest, Vol 1 #127 - 3 msgs >Date: Tue, 6 Nov 2001 12:00:04 -0500 > > >Send BiO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > >To subscribe or unsubscribe via the web, visit > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board >or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org >You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > >When replying, please edit your Subject line so it is more specific than >"Re: Contents of BiO_Bulletin_Board digest...") > > >Today's Topics: > > 1. Re: BiO_Bulletin_Board digest, Vol 1 #126 - 3 msgs (Louis Pilli) > 2. Good OOP and Java Book (Tanya Vavouri) > 3. Re: Good OOP and Java Book (John Scheiderer) > >--__--__-- > >Message: 1 >Date: Mon, 05 Nov 2001 14:58:10 -0500 >Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #126 - 3 msgs >From: Louis Pilli >To: >Reply-To: bio_bulletin_board at bioinformatics.org > >on 11/5/01 12:00 PM, bio_bulletin_board-admin at bioinformatics.org at >bio_bulletin_board-admin at bioinformatics.org wrote: > > > > > Send BiO_Bulletin_Board maillist submissions to > > bio_bulletin_board at bioinformatics.org > > > > To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > or, via email, send a message with subject or body 'help' to > > bio_bulletin_board-request at bioinformatics.org > > You can reach the person managing the list at > > bio_bulletin_board-admin at bioinformatics.org > > > > When replying, please edit your Subject line so it is more specific than > > "Re: Contents of BiO_Bulletin_Board digest...") > > > > > > Today's Topics: > > > > 1. Re: RE: [BiO BB] Demo projects in pharmacogenomics (j kamesh) > > 2. RE: Demo projects in pharmacogenomics (Marcos Oliveira de Carvalho) > > 3. RE: Re: RE: [BiO BB] Demo projects in pharmacogenomics (Ravi >Mayreddy) > > > > -- __--__-- > > > > Message: 1 > > Date: 5 Nov 2001 12:05:55 -0000 > > From: "j kamesh" > > Reply-To: "j kamesh" > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > charset=iso-8859-1 > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > > > Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > > biosciences then my MCA, i have 3 yrs in IT now im looking for some > > opportinuties in bioinformatics.pls help me so that i can join as some >trainy > > or some thing.suggest me some sites for free tutorials on bioinformatics > > tools. some e books, news letters sites. > > -Regs > > j.kamesh > > > > On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > >> WE are planning to set up a training class on > >> pharmacogenomics. Can you, > >> especially Kiran, suggest software, and other relavent > >> info. > >> > >> Thanks, > >> Ravi > >> > >> -----Original Message----- > >> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > >> Sent: Friday, November 02, 2001 4:40 AM > >> To: bio_bulletin_board at bioinformatics.org > >> Subject: [BiO BB] Demo projects in pharmacogenomics > >> > >> > >> Hi! all, > >> > >> Kindly suggest me a demo project in the area of > >> pharmacogenomics.And Kindly enlist the steps to do it. > >> > >> I have the necessary software packages to do the same. > >> Thanks in advance. > >> > >> -Kiran > >> > >> > >> > >> > >> > >> > >> __________________________________________________ > >> Do You Yahoo!? > >> Find a job, post your resume. > >> http://careers.yahoo.com > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - > >> BiO_Bulletin_Board at bioinformatics.org > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > >> board > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - > >> BiO_Bulletin_Board at bioinformatics.org > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > >> board > >> > > > > > > > > -- __--__-- > > > > Message: 2 > > From: "Marcos Oliveira de Carvalho" > > To: > > Subject: RE: [BiO BB] Demo projects in pharmacogenomics > > Date: Mon, 5 Nov 2001 12:25:37 -0200 > > charset="iso-8859-1" > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > Hi Kamesh > > > > Take a look: > > http://linkage.rockefeller.edu/wli/bioinfocourse/ > > http://www.math.tau.ac.il/~rshamir/algmb/algmb98.html > > http://www.sequenceanalysis.com/ > > http://www.agr.kuleuven.ac.be/vakken/i287/bioinformatica.htm > > http://www.hgmp.mrc.ac.uk/CCP11/ > > http://www.uni-mainz.de/~cfrosch/bc4s/example.html > > http://www.cse.ucsc.edu/classes/cmpe177/ > > http://bioinfo.mbb.yale.edu/mbb447b-99/ > > http://www.cse.ucsc.edu/classes/cmp243/ > > > > Best regards > > Marcos de Carvalho > > > > > > > > ----- Original Message ----- > > From: "j kamesh" > > To: > > Sent: Monday, November 05, 2001 10:05 AM > > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > > > > >> > >> Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > > biosciences then my MCA, i have 3 yrs in IT now im looking for some > > opportinuties in bioinformatics.pls help me so that i can join as some > > trainy or some thing.suggest me some sites for free tutorials on > > bioinformatics tools. some e books, news letters sites. > >> -Regs > >> j.kamesh > >> > >> On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > >>> WE are planning to set up a training class on > >>> pharmacogenomics. Can you, > >>> especially Kiran, suggest software, and other relavent > >>> info. > >>> > >>> Thanks, > >>> Ravi > >>> > >>> -----Original Message----- > >>> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > >>> Sent: Friday, November 02, 2001 4:40 AM > >>> To: bio_bulletin_board at bioinformatics.org > >>> Subject: [BiO BB] Demo projects in pharmacogenomics > >>> > >>> > >>> Hi! all, > >>> > >>> Kindly suggest me a demo project in the area of > >>> pharmacogenomics.And Kindly enlist the steps to do it. > >>> > >>> I have the necessary software packages to do the same. > >>> Thanks in advance. > >>> > >>> -Kiran > >>> > >>> > >>> > >>> > >>> > >>> > >>> __________________________________________________ > >>> Do You Yahoo!? > >>> Find a job, post your resume. > >>> http://careers.yahoo.com > >>> > >>> _______________________________________________ > >>> BiO_Bulletin_Board maillist - > >>> BiO_Bulletin_Board at bioinformatics.org > >>> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > >>> board > >>> > >>> _______________________________________________ > >>> BiO_Bulletin_Board maillist - > >>> BiO_Bulletin_Board at bioinformatics.org > >>> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > >>> board > >>> > >> > >> > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >> > >> > > > > > > -- __--__-- > > > > Message: 3 > > From: Ravi Mayreddy > > To: "'bio_bulletin_board at bioinformatics.org'" > > > > Subject: RE: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > Date: Mon, 5 Nov 2001 09:23:49 -0500 > > charset="iso-8859-1" > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > Where are you located? > > > > -ravi > > > > -----Original Message----- > > From: j kamesh [mailto:jkwaran at rediffmail.com] > > Sent: Monday, November 05, 2001 7:06 AM > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > > > > > > > Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > > biosciences then my MCA, i have 3 yrs in IT now im looking for some > > opportinuties in bioinformatics.pls help me so that i can join as some > > trainy or some thing.suggest me some sites for free tutorials on > > bioinformatics tools. some e books, news letters sites. > > -Regs > > j.kamesh > > > > On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > >> WE are planning to set up a training class on > >> pharmacogenomics. Can you, > >> especially Kiran, suggest software, and other relavent > >> info. > >> > >> Thanks, > >> Ravi > >> > >> -----Original Message----- > >> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > >> Sent: Friday, November 02, 2001 4:40 AM > >> To: bio_bulletin_board at bioinformatics.org > >> Subject: [BiO BB] Demo projects in pharmacogenomics > >> > >> > >> Hi! all, > >> > >> Kindly suggest me a demo project in the area of > >> pharmacogenomics.And Kindly enlist the steps to do it. > >> > >> I have the necessary software packages to do the same. > >> Thanks in advance. > >> > >> -Kiran > >> > >> > >> > >> > >> > >> > >> __________________________________________________ > >> Do You Yahoo!? > >> Find a job, post your resume. > >> http://careers.yahoo.com > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - > >> BiO_Bulletin_Board at bioinformatics.org > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > >> board > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - > >> BiO_Bulletin_Board at bioinformatics.org > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > >> board > >> > > > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > -- __--__-- > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > -- __--__-- -- > > > > End of BiO_Bulletin_Board Digest > > >Biotech and Pharma opportunities in Canada! > >Visit http://www.exxcalibur.net and register with us. > > > >--__--__-- > >Message: 2 >From: "Tanya Vavouri" >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Good OOP and Java Book >Date: Tue, 06 Nov 2001 13:56:47 +0000 >Reply-To: bio_bulletin_board at bioinformatics.org > >Hi, > >I am starting a bioinformatics project in which I'll develop a program in >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am >looking for a good book that will introduce me to OOP and then teach me >Java. Are there any books that you would recommend ? I have found some >titles but I'd like to have some opinions as well. > >Thanks in advance, >Tanya > > >_________________________________________________________________ >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > >--__--__-- > >Message: 3 >From: "John Scheiderer" >To: >Cc: >Subject: Re: [BiO BB] Good OOP and Java Book >Date: Tue, 6 Nov 2001 09:37:44 -0500 >Reply-To: bio_bulletin_board at bioinformatics.org > > >------=_NextPart_001_0000_01C166A6.AFAC6640 >Content-Type: text/plain; charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > >Just Java 2 by Peter Van Der Linden is an excellent book to learn Java (a= >nd does cover some OOP). > >http://www.amazon.com/exec/obidos/ASIN/0130105341/qid=3D1005057200/sr=3D8= >-1/ref=3Dsr_8_7_1/104-7110682-2029545 > >----- Original Message ----- >From: Tanya Vavouri >Sent: Tuesday, November 06, 2001 9:13 AM >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Good OOP and Java Book > >Hi, > >I am starting a bioinformatics project in which I'll develop a program in >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am >looking for a good book that will introduce me to OOP and then teach me >Java. Are there any books that you would recommend ? I have found some >titles but I'd like to have some opinions as well. > >Thanks in advance, >Tanya > > >_________________________________________________________________ >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.as= >p > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_boardGet more fro= >m the Web. FREE MSN Explorer download : http://explorer.msn.com > >------=_NextPart_001_0000_01C166A6.AFAC6640 >Content-Type: text/html; charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > >
Just Java 2 by= > Peter Van Der Linden is an excellent book to learn Java (and does c= >over some OOP).
 
V> 
; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px"> <= >DIV style=3D"FONT: 10pt Arial">----- Original Message -----
yle=3D"BACKGROUND: #e4e4e4; FONT: 10pt Arial; COLOR: black">From: = >Tanya Vavouri
Sent: Tuesday,= > November 06, 2001 9:13 AM
To:B> bio_bulletin_board at bioinformatics.org
rial">Subject: [BiO BB] Good OOP and Java Book
 DIV>Hi,

I am starting a bioinformatics project in which I'll devel= >op a program in
Java. Since I have no experience in Java and OOP (only= > C/Perl/VB) I am
looking for a good book that will introduce me to OOP= > and then teach me
Java. Are there any books that you would recommend = >? I have found some
titles but I'd like to have some opinions as well.= >

Thanks in advance,
Tanya


__________________________= >_______________________________________
Get your FREE download of MSN = >Explorer at http://explorer.msn.com/intl.asp


_________________= >______________________________
BiO_Bulletin_Board maillist  -&nbs= >p; BiO_Bulletin_Board at bioinformatics.org
http://bioinformatics.org/mai= >lman/listinfo/bio_bulletin_board


ear=3Dall>
Get more from the Web. FREE MSN Explorer download : f=3D'http://explorer.msn.com'>http://explorer.msn.com

> >------=_NextPart_001_0000_01C166A6.AFAC6640-- > > > >--__--__-- > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >--__--__---- > >End of BiO_Bulletin_Board Digest _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From tvavouri at hotmail.com Wed Nov 7 04:52:40 2001 From: tvavouri at hotmail.com (Tanya Vavouri) Date: Wed, 07 Nov 2001 09:52:40 +0000 Subject: [BiO BB] Good OOP and Java Book Message-ID: Thank you all for your reccommendations, they were very helpful. Tanya >From: "Klicker, Kyle R" >Reply-To: bio_bulletin_board at bioinformatics.org >To: "'bio_bulletin_board at bioinformatics.org'" > >Subject: RE: [BiO BB] Good OOP and Java Book >Date: Tue, 06 Nov 2001 09:02:36 -0800 > >Personally, I like the Deitel and Deitel books, but that's just me. They >cover >OOP well I think. > >Hope this helps, > >Kyle > >-----Original Message----- >From: Tanya Vavouri [mailto:tvavouri at hotmail.com] >Sent: Tuesday, November 06, 2001 5:57 AM >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Good OOP and Java Book > > >Hi, > >I am starting a bioinformatics project in which I'll develop a program in >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am >looking for a good book that will introduce me to OOP and then teach me >Java. Are there any books that you would recommend ? I have found some >titles but I'd like to have some opinions as well. > >Thanks in advance, >Tanya > > >_________________________________________________________________ >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From ng at mbi.ucla.edu Wed Nov 7 13:36:46 2001 From: ng at mbi.ucla.edu (Ho-Leung Ng) Date: Wed, 7 Nov 2001 10:36:46 -0800 (PST) Subject: [BiO BB] Unix or Linux? Compilers In-Reply-To: <200111071700.MAA08313@www.bioinformatics.org> Message-ID: Many labs use Alphas because of their superlative performance, but the latest Athlons may be faster now. Linux is probably the way to go, but you may want to look into commercial compilers because gcc can be as much as 50% slower than commercial alternatives. Intel has just released C/C++/Fortran compilers for linux that are free for noncommercial use. I've heard they are very impressive. Ho-Leung Ng UC Berkeley From tdhoufek at unity.ncsu.edu Wed Nov 7 14:14:17 2001 From: tdhoufek at unity.ncsu.edu (T.D. Houfek) Date: Wed, 7 Nov 2001 14:14:17 -0500 (EST) Subject: [BiO BB] Unix or Linux In-Reply-To: <20011106173747.84595.qmail@web14506.mail.yahoo.com> Message-ID: Hi Peri, We've been using (Red Hat) Linux at our lab for the last two years... currently we've got it on 6 Dell PowerEdge servers and on a Dell Inspiron laptop. It has served us well. At one point someone from a neighboring lab said they thought a Solaris box would work better for BLAST searches, since the chipset is optimized for non-floating-point operations I guess, but when we held a (not very rigorous) "race" our Dell/Linux machine seemed to outperform their Solaris machine. Hope this helps, T.D. T.D. Houfek system administrator NCSU Fungal Genomics Laboratory (919)513-0025 tdhoufek at unity.ncsu.edu On Tue, 6 Nov 2001, Peri Suraj wrote: > Hi group, > I am on a survey and also to know what is the type of > computing environment, big and famous labs in > bioinformatics prefer. > > Which server ( A unix or Linux) you prefer,that has > all the important databases for critical research > purpose, considering robustness of the system. > > 1. UNIX ( Digital, Solaris, IRIX that are proprietory > and robust) > 2. LINUX( Free, widely used and flexible) > > > Folks, what would you prefer? > Please post your suggestion and views ! > > cheers > sp > > > > ===== > PIL/CEBI/SDU/DK > > __________________________________________________ > Do You Yahoo!? > Find a job, post your resume. > http://careers.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From jpostlethwaite at unexmail.ucdavis.edu Wed Nov 7 16:08:21 2001 From: jpostlethwaite at unexmail.ucdavis.edu (Judy Postlethwaite) Date: Wed, 7 Nov 2001 13:08:21 -0800 Subject: [BiO BB] UC Davis Extension Bio Courses Message-ID: <8031E71E9F9FD41198AC00A0246D484C018A09D4@unexmail.ucdavis.edu> <<013-409 Biotechnology PR.doc>> Judy Postlethwaite Distribution Planning Specialist UC Davis Extension 1333 Research Park Dr Davis, CA 95616 (530) 752-9441 (503) 754-5094 fax jpostlethwaite at unexmail.ucdavis.edu -------------- next part -------------- A non-text attachment was scrubbed... Name: 013-409 Biotechnology PR.doc Type: application/msword Size: 26112 bytes Desc: not available URL: From Pratap.Kotala at ndsu.nodak.edu Wed Nov 7 18:59:36 2001 From: Pratap.Kotala at ndsu.nodak.edu (Pratap Kotala) Date: Wed, 7 Nov 2001 17:59:36 -0600 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #128 - 6 msgs In-Reply-To: <200111071700.MAA08320@www.bioinformatics.org> References: <200111071700.MAA08320@www.bioinformatics.org> Message-ID: <200111072359.fA7NxYf02653@smtp1.ndsu.nodak.edu> Hi I believe "Thinking in Java" by Bruce Eckel should be a very good book for someone with C background. It not only introduces you to Java but, also to the OO paradigm. Also, this is a free electronic book available on the web at http://www.mindview.net/Books/TIJ/. Check it out. You might like it. -Pratap On Wednesday 07 November 2001 11:00 am, you wrote: > Send BiO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of BiO_Bulletin_Board digest...") > > > Today's Topics: > > 1. RE: Good OOP and Java Book (Klicker, Kyle R) > 2. RE: Good OOP and Java Book (Jennifer Steinbachs) > 3. Re: Unix or Linux (Peri Suraj) > 4. RE: Unix or Linux (Joel Dudley) > 5. Re: BiO_Bulletin_Board digest, Vol 1 #127 - 3 msgs (Animesh Sharma) > 6. RE: Good OOP and Java Book (Tanya Vavouri) > > --__--__-- > > Message: 1 > Date: Tue, 06 Nov 2001 09:02:36 -0800 > From: "Klicker, Kyle R" > Subject: RE: [BiO BB] Good OOP and Java Book > To: "'bio_bulletin_board at bioinformatics.org'" > > Reply-To: bio_bulletin_board at bioinformatics.org > > Personally, I like the Deitel and Deitel books, but that's just me. They > cover OOP well I think. > > Hope this helps, > > Kyle > > -----Original Message----- > From: Tanya Vavouri [mailto:tvavouri at hotmail.com] > Sent: Tuesday, November 06, 2001 5:57 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Good OOP and Java Book > > > Hi, > > I am starting a bioinformatics project in which I'll develop a program in > Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am > looking for a good book that will introduce me to OOP and then teach me > Java. Are there any books that you would recommend ? I have found some > titles but I'd like to have some opinions as well. > > Thanks in advance, > Tanya > > > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > --__--__-- > > Message: 2 > Date: Tue, 6 Nov 2001 11:09:46 -0600 (CST) > From: Jennifer Steinbachs > To: "'bio_bulletin_board at bioinformatics.org'" > Subject: RE: [BiO BB] Good OOP and > Java Book > Reply-To: bio_bulletin_board at bioinformatics.org > > > > For OOP, I was encouraged to read: > > G. Booch. Object-oriented analysis and design with applications. > > I have the 2nd edition (ISBN 0905353402) but there is probably a newer > version out by now. > > -jennifer > > On Tue, 6 Nov 2001, Klicker, Kyle R wrote: > >Personally, I like the Deitel and Deitel books, but that's just me. They > > cover OOP well I think. > > > >Hope this helps, > > > >Kyle > > > >-----Original Message----- > > From: Tanya Vavouri [mailto:tvavouri at hotmail.com] > > >Sent: Tuesday, November 06, 2001 5:57 AM > >To: bio_bulletin_board at bioinformatics.org > >Subject: [BiO BB] Good OOP and Java Book > > > > > >Hi, > > > >I am starting a bioinformatics project in which I'll develop a program in > >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am > >looking for a good book that will introduce me to OOP and then teach me > >Java. Are there any books that you would recommend ? I have found some > >titles but I'd like to have some opinions as well. > > > >Thanks in advance, > >Tanya > > > > > >_________________________________________________________________ > >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > ----------------------------------- > J. Steinbachs, Ph.D. > Computational Biologist > http://compbiology.org > ----------------------------------- > > > --__--__-- > > Message: 3 > Date: Tue, 6 Nov 2001 09:37:46 -0800 (PST) > From: Peri Suraj > Subject: Re: [BiO BB] Unix or Linux > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > Hi group, > I am on a survey and also to know what is the type of > computing environment, big and famous labs in > bioinformatics prefer. > > Which server ( A unix or Linux) you prefer,that has > all the important databases for critical research > purpose, considering robustness of the system. > > 1. UNIX ( Digital, Solaris, IRIX that are proprietory > and robust) > 2. LINUX( Free, widely used and flexible) > > > Folks, what would you prefer? > Please post your suggestion and views ! > > cheers > sp > > > > ===== > PIL/CEBI/SDU/DK > > __________________________________________________ > Do You Yahoo!? > Find a job, post your resume. > http://careers.yahoo.com > > --__--__-- > > Message: 4 > From: Joel Dudley > To: "'bio_bulletin_board at bioinformatics.org'" > > Subject: RE: [BiO BB] Unix or Linux > Date: Tue, 6 Nov 2001 15:10:02 -0700 > charset="iso-8859-1" > Reply-To: bio_bulletin_board at bioinformatics.org > > well linux of course!! all NCBI libraries are available for linux. Also, > most major databases like MySQL and oracel will run on it. > > -----Original Message----- > From: Peri Suraj [mailto:bioinfo_india at yahoo.com] > Sent: Tuesday, November 06, 2001 10:38 AM > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Unix or Linux > > > Hi group, > I am on a survey and also to know what is the type of > computing environment, big and famous labs in > bioinformatics prefer. > > Which server ( A unix or Linux) you prefer,that has > all the important databases for critical research > purpose, considering robustness of the system. > > 1. UNIX ( Digital, Solaris, IRIX that are proprietory > and robust) > 2. LINUX( Free, widely used and flexible) > > > Folks, what would you prefer? > Please post your suggestion and views ! > > cheers > sp > > > > ===== > PIL/CEBI/SDU/DK > > __________________________________________________ > Do You Yahoo!? > Find a job, post your resume. > http://careers.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > --__--__-- > > Message: 5 > From: "Animesh Sharma" > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #127 - 3 msgs > Date: Wed, 07 Nov 2001 09:00:53 > Reply-To: bio_bulletin_board at bioinformatics.org > > hello to all the members of bulletin board, > > i just joined this community and i feel it is a good place to share views > and tools :) . > i m a student of bioinformatics in JNU, delhi and wud like to have some > help on a good book on ALGORITHM used in bioinformatics like SmithWaterman > , Chous-Fasmann etc... or any links which explain this . > > thanks alot in advance > > ani > > ********************************************************************** > the answer lies in genome > ********************************************************************** > > dr.animesh sharma > bioinformatics centre > JNU,Delhi > > > > From: bio_bulletin_board-admin at bioinformatics.org > > >Reply-To: bio_bulletin_board at bioinformatics.org > >To: bio_bulletin_board at bioinformatics.org > >Subject: BiO_Bulletin_Board digest, Vol 1 #127 - 3 msgs > >Date: Tue, 6 Nov 2001 12:00:04 -0500 > > > > > >Send BiO_Bulletin_Board maillist submissions to > > bio_bulletin_board at bioinformatics.org > > > >To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >or, via email, send a message with subject or body 'help' to > > bio_bulletin_board-request at bioinformatics.org > >You can reach the person managing the list at > > bio_bulletin_board-admin at bioinformatics.org > > > >When replying, please edit your Subject line so it is more specific than > >"Re: Contents of BiO_Bulletin_Board digest...") > > > > > >Today's Topics: > > > > 1. Re: BiO_Bulletin_Board digest, Vol 1 #126 - 3 msgs (Louis Pilli) > > 2. Good OOP and Java Book (Tanya Vavouri) > > 3. Re: Good OOP and Java Book (John Scheiderer) > > > >-- __--__-- > > > >Message: 1 > >Date: Mon, 05 Nov 2001 14:58:10 -0500 > >Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #126 - 3 msgs > > From: Louis Pilli > > >To: > >Reply-To: bio_bulletin_board at bioinformatics.org > > > >on 11/5/01 12:00 PM, bio_bulletin_board-admin at bioinformatics.org at > > > >bio_bulletin_board-admin at bioinformatics.org wrote: > > > Send BiO_Bulletin_Board maillist submissions to > > > bio_bulletin_board at bioinformatics.org > > > > > > To subscribe or unsubscribe via the web, visit > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > or, via email, send a message with subject or body 'help' to > > > bio_bulletin_board-request at bioinformatics.org > > > You can reach the person managing the list at > > > bio_bulletin_board-admin at bioinformatics.org > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of BiO_Bulletin_Board digest...") > > > > > > > > > Today's Topics: > > > > > > 1. Re: RE: [BiO BB] Demo projects in pharmacogenomics (j kamesh) > > > 2. RE: Demo projects in pharmacogenomics (Marcos Oliveira de Carvalho) > > > 3. RE: Re: RE: [BiO BB] Demo projects in pharmacogenomics (Ravi > > > >Mayreddy) > > > > > -- __--__-- > > > > > > Message: 1 > > > Date: 5 Nov 2001 12:05:55 -0000 > > > From: "j kamesh" > > > Reply-To: "j kamesh" > > > To: bio_bulletin_board at bioinformatics.org > > > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > > charset=iso-8859-1 > > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > > > > > > Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > > > biosciences then my MCA, i have 3 yrs in IT now im looking for some > > > opportinuties in bioinformatics.pls help me so that i can join as some > > > >trainy > > > > > or some thing.suggest me some sites for free tutorials on > > > bioinformatics tools. some e books, news letters sites. > > > -Regs > > > j.kamesh > > > > > > On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > > >> WE are planning to set up a training class on > > >> pharmacogenomics. Can you, > > >> especially Kiran, suggest software, and other relavent > > >> info. > > >> > > >> Thanks, > > >> Ravi > > >> > > >> -----Original Message----- > > >> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > > >> Sent: Friday, November 02, 2001 4:40 AM > > >> To: bio_bulletin_board at bioinformatics.org > > >> Subject: [BiO BB] Demo projects in pharmacogenomics > > >> > > >> > > >> Hi! all, > > >> > > >> Kindly suggest me a demo project in the area of > > >> pharmacogenomics.And Kindly enlist the steps to do it. > > >> > > >> I have the necessary software packages to do the same. > > >> Thanks in advance. > > >> > > >> -Kiran > > >> > > >> > > >> > > >> > > >> > > >> > > >> __________________________________________________ > > >> Do You Yahoo!? > > >> Find a job, post your resume. > > >> http://careers.yahoo.com > > >> > > >> _______________________________________________ > > >> BiO_Bulletin_Board maillist - > > >> BiO_Bulletin_Board at bioinformatics.org > > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > >> board > > >> > > >> _______________________________________________ > > >> BiO_Bulletin_Board maillist - > > >> BiO_Bulletin_Board at bioinformatics.org > > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > >> board > > > > > > -- __--__-- > > > > > > Message: 2 > > > From: "Marcos Oliveira de Carvalho" > > > To: > > > Subject: RE: [BiO BB] Demo projects in pharmacogenomics > > > Date: Mon, 5 Nov 2001 12:25:37 -0200 > > > charset="iso-8859-1" > > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > > > Hi Kamesh > > > > > > Take a look: > > > http://linkage.rockefeller.edu/wli/bioinfocourse/ > > > http://www.math.tau.ac.il/~rshamir/algmb/algmb98.html > > > http://www.sequenceanalysis.com/ > > > http://www.agr.kuleuven.ac.be/vakken/i287/bioinformatica.htm > > > http://www.hgmp.mrc.ac.uk/CCP11/ > > > http://www.uni-mainz.de/~cfrosch/bc4s/example.html > > > http://www.cse.ucsc.edu/classes/cmpe177/ > > > http://bioinfo.mbb.yale.edu/mbb447b-99/ > > > http://www.cse.ucsc.edu/classes/cmp243/ > > > > > > Best regards > > > Marcos de Carvalho > > > > > > > > > > > > ----- Original Message ----- > > > From: "j kamesh" > > > To: > > > Sent: Monday, November 05, 2001 10:05 AM > > > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > > > > >> Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > > > > > > biosciences then my MCA, i have 3 yrs in IT now im looking for some > > > opportinuties in bioinformatics.pls help me so that i can join as some > > > trainy or some thing.suggest me some sites for free tutorials on > > > bioinformatics tools. some e books, news letters sites. > > > > > >> -Regs > > >> j.kamesh > > >> > > >> On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > > >>> WE are planning to set up a training class on > > >>> pharmacogenomics. Can you, > > >>> especially Kiran, suggest software, and other relavent > > >>> info. > > >>> > > >>> Thanks, > > >>> Ravi > > >>> > > >>> -----Original Message----- > > >>> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > > >>> Sent: Friday, November 02, 2001 4:40 AM > > >>> To: bio_bulletin_board at bioinformatics.org > > >>> Subject: [BiO BB] Demo projects in pharmacogenomics > > >>> > > >>> > > >>> Hi! all, > > >>> > > >>> Kindly suggest me a demo project in the area of > > >>> pharmacogenomics.And Kindly enlist the steps to do it. > > >>> > > >>> I have the necessary software packages to do the same. > > >>> Thanks in advance. > > >>> > > >>> -Kiran > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> __________________________________________________ > > >>> Do You Yahoo!? > > >>> Find a job, post your resume. > > >>> http://careers.yahoo.com > > >>> > > >>> _______________________________________________ > > >>> BiO_Bulletin_Board maillist - > > >>> BiO_Bulletin_Board at bioinformatics.org > > >>> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > >>> board > > >>> > > >>> _______________________________________________ > > >>> BiO_Bulletin_Board maillist - > > >>> BiO_Bulletin_Board at bioinformatics.org > > >>> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > >>> board > > >> > > >> _______________________________________________ > > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > -- __--__-- > > > > > > Message: 3 > > > From: Ravi Mayreddy > > > To: "'bio_bulletin_board at bioinformatics.org'" > > > > > > Subject: RE: [BiO BB] Re: RE: [BiO BB] Demo projects in > > > pharmacogenomics Date: Mon, 5 Nov 2001 09:23:49 -0500 > > > charset="iso-8859-1" > > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > > > Where are you located? > > > > > > -ravi > > > > > > -----Original Message----- > > > From: j kamesh [mailto:jkwaran at rediffmail.com] > > > Sent: Monday, November 05, 2001 7:06 AM > > > To: bio_bulletin_board at bioinformatics.org > > > Subject: [BiO BB] Re: RE: [BiO BB] Demo projects in pharmacogenomics > > > > > > > > > > > > Hi This J.Kamesh, i am fresh to bioinformatics, i have done my BSc in > > > biosciences then my MCA, i have 3 yrs in IT now im looking for some > > > opportinuties in bioinformatics.pls help me so that i can join as some > > > trainy or some thing.suggest me some sites for free tutorials on > > > bioinformatics tools. some e books, news letters sites. > > > -Regs > > > j.kamesh > > > > > > On Fri, 02 Nov 2001 Ravi Mayreddy wrote : > > >> WE are planning to set up a training class on > > >> pharmacogenomics. Can you, > > >> especially Kiran, suggest software, and other relavent > > >> info. > > >> > > >> Thanks, > > >> Ravi > > >> > > >> -----Original Message----- > > >> From: Ayyagari Kiran [mailto:kiran_ayyagari at yahoo.com] > > >> Sent: Friday, November 02, 2001 4:40 AM > > >> To: bio_bulletin_board at bioinformatics.org > > >> Subject: [BiO BB] Demo projects in pharmacogenomics > > >> > > >> > > >> Hi! all, > > >> > > >> Kindly suggest me a demo project in the area of > > >> pharmacogenomics.And Kindly enlist the steps to do it. > > >> > > >> I have the necessary software packages to do the same. > > >> Thanks in advance. > > >> > > >> -Kiran > > >> > > >> > > >> > > >> > > >> > > >> > > >> __________________________________________________ > > >> Do You Yahoo!? > > >> Find a job, post your resume. > > >> http://careers.yahoo.com > > >> > > >> _______________________________________________ > > >> BiO_Bulletin_Board maillist - > > >> BiO_Bulletin_Board at bioinformatics.org > > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > >> board > > >> > > >> _______________________________________________ > > >> BiO_Bulletin_Board maillist - > > >> BiO_Bulletin_Board at bioinformatics.org > > >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > > >> board > > > > > > _______________________________________________ > > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > > > -- __--__-- > > > > > > _______________________________________________ > > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > -- __--__-- -- > > > > > > End of BiO_Bulletin_Board Digest > > > >Biotech and Pharma opportunities in Canada! > > > >Visit http://www.exxcalibur.net and register with us. > > > > > > > >-- __--__-- > > > >Message: 2 > > From: "Tanya Vavouri" > > >To: bio_bulletin_board at bioinformatics.org > >Subject: [BiO BB] Good OOP and Java Book > >Date: Tue, 06 Nov 2001 13:56:47 +0000 > >Reply-To: bio_bulletin_board at bioinformatics.org > > > >Hi, > > > >I am starting a bioinformatics project in which I'll develop a program in > >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am > >looking for a good book that will introduce me to OOP and then teach me > >Java. Are there any books that you would recommend ? I have found some > >titles but I'd like to have some opinions as well. > > > >Thanks in advance, > >Tanya > > > > > >_________________________________________________________________ > >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > > > > >-- __--__-- > > > >Message: 3 > > From: "John Scheiderer" > > >To: > >Cc: > >Subject: Re: [BiO BB] Good OOP and Java Book > >Date: Tue, 6 Nov 2001 09:37:44 -0500 > >Reply-To: bio_bulletin_board at bioinformatics.org > > > > > >------=_NextPart_001_0000_01C166A6.AFAC6640 > >Content-Type: text/plain; charset="iso-8859-1" > >Content-Transfer-Encoding: quoted-printable > > > >Just Java 2 by Peter Van Der Linden is an excellent book to learn Java (a= > >nd does cover some OOP). > > > >http://www.amazon.com/exec/obidos/ASIN/0130105341/qid=3D1005057200/sr=3D8= > >-1/ref=3Dsr_8_7_1/104-7110682-2029545 > > > >----- Original Message ----- > > From: Tanya Vavouri > > >Sent: Tuesday, November 06, 2001 9:13 AM > >To: bio_bulletin_board at bioinformatics.org > >Subject: [BiO BB] Good OOP and Java Book > > > >Hi, > > > >I am starting a bioinformatics project in which I'll develop a program in > >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am > >looking for a good book that will introduce me to OOP and then teach me > >Java. Are there any books that you would recommend ? I have found some > >titles but I'd like to have some opinions as well. > > > >Thanks in advance, > >Tanya > > > > > >_________________________________________________________________ > >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.as= > >p > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >http://bioinformatics.org/mailman/listinfo/bio_bulletin_boardGet more fro= > >m the Web. FREE MSN Explorer download : http://explorer.msn.com > > > >------=_NextPart_001_0000_01C166A6.AFAC6640 > >Content-Type: text/html; charset="iso-8859-1" > >Content-Transfer-Encoding: quoted-printable > > > >
Just Java 2 by= > > Peter Van Der Linden is an excellent book to learn Java (and does c= > >over some OOP).
 
>V> 
>; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px"> <= > >DIV style=3D"FONT: 10pt Arial">----- Original Message -----
>yle=3D"BACKGROUND: #e4e4e4; FONT: 10pt Arial; COLOR: black">From: = > >Tanya Vavouri
Sent: Tuesday,= > > November 06, 2001 9:13 AM
> Arial">To: bio_bulletin_board at bioinformatics.org
> style=3D"FONT: 10pt A= rial">Subject: [BiO BB] Good OOP and Java > > Book
 Hi,

I am starting a bioinformatics > > project in which I'll devel= op a program in
Java. Since I have no > > experience in Java and OOP (only= C/Perl/VB) I am
looking for a good > > book that will introduce me to OOP= and then teach me
Java. Are there > > any books that you would recommend = ? I have found some
titles but > > I'd like to have some opinions as well.=

Thanks in > > advance,
Tanya


__________________________= > > _______________________________________
Get your FREE download of MSN > > = Explorer at > > http://explorer.msn.com/intl.asp


_________________= > > ______________________________
BiO_Bulletin_Board maillist  > > -&nbs= p; > > BiO_Bulletin_Board at bioinformatics.org
http://bioinformatics.org/mai= > > lman/listinfo/bio_bulletin_board


> cl= ear=3Dall>
Get more from the Web. FREE MSN Explorer download : > hre= f=3D'http://explorer.msn.com'>http://explorer.msn.com

> > > >------=_NextPart_001_0000_01C166A6.AFAC6640-- > > > > > > > >-- __--__-- > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > >-- __--__-- -- > > > >End of BiO_Bulletin_Board Digest > > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > > --__--__-- > > Message: 6 > From: "Tanya Vavouri" > To: bio_bulletin_board at bioinformatics.org > Subject: RE: [BiO BB] Good OOP and Java Book > Date: Wed, 07 Nov 2001 09:52:40 +0000 > Reply-To: bio_bulletin_board at bioinformatics.org > > Thank you all for your reccommendations, they were very helpful. > > Tanya > > > > > From: "Klicker, Kyle R" > > >Reply-To: bio_bulletin_board at bioinformatics.org > >To: "'bio_bulletin_board at bioinformatics.org'" > > > >Subject: RE: [BiO BB] Good OOP and Java Book > >Date: Tue, 06 Nov 2001 09:02:36 -0800 > > > >Personally, I like the Deitel and Deitel books, but that's just me. They > >cover > >OOP well I think. > > > >Hope this helps, > > > >Kyle > > > >-----Original Message----- > > From: Tanya Vavouri [mailto:tvavouri at hotmail.com] > > >Sent: Tuesday, November 06, 2001 5:57 AM > >To: bio_bulletin_board at bioinformatics.org > >Subject: [BiO BB] Good OOP and Java Book > > > > > >Hi, > > > >I am starting a bioinformatics project in which I'll develop a program in > >Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am > >looking for a good book that will introduce me to OOP and then teach me > >Java. Are there any books that you would recommend ? I have found some > >titles but I'd like to have some opinions as well. > > > >Thanks in advance, > >Tanya > > > > > >_________________________________________________________________ > >Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > --__--__---- > > End of BiO_Bulletin_Board Digest From jwester at sgi1.chemie.uni-hamburg.de Thu Nov 8 02:55:54 2001 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Thu, 08 Nov 2001 08:55:54 +0100 Subject: [BiO BB] Unix or Linux? Compilers References: Message-ID: <3BEA3A8A.F4011BEA@sgi1.chemie.uni-hamburg.de> Ho-Leung Ng wrote: > > Many labs use Alphas because of their superlative performance, but > the latest Athlons may be faster now. Linux is probably the way to go, but Alpha is 64bit technology, it is still faster than any 32bit processor (sometimes depending on application). SuSE sells it's Linux distribution for Alpha processors with the Compaq C/C++ and Fortran compilers. They are said to be among the best compilers available. > you may want to look into commercial compilers because gcc can be as much > as 50% slower than commercial alternatives. Intel has just released > C/C++/Fortran compilers for linux that are free for noncommercial use. > I've heard they are very impressive. The Intel compilers are not compatible with certain GNU extensions for C/C++, so the Linux kernel doesn't compile with it (afaik). If you use ansi C/C++ the might be okay, they are avalabble for Itanium too, or they will be soon. BTW Intel bought the Alpha processor design, including compiler technology from Compaq. jcw -- Jan-C. Westermann jwester at sgi1.chemie.uni-hamburg.de Nota bene: wenn Word f?r L?ngeres geeignet w?re, w?rde es schlie?lich nicht Word, sondern Sentence, Page oder Article hei?en ;-) Matthias M?hlich in dctt From naitik.kothari at sgib.com Thu Nov 8 07:02:03 2001 From: naitik.kothari at sgib.com (naitik.kothari at sgib.com) Date: Thu, 8 Nov 2001 17:32:03 +0530 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #127 - 3 msgs Message-ID: <49256AFE.006DB211.00@gatok001.jp.socgen.com> Hi You can refer to the following books. 1. Biological Sequence analysis By: R. Durbin S. Eddy A. Krogh G.Mitchison This is for all kind of algorithms. 2. Prediction of protein structure conformation Edited By: Gerald D. Fasman Plenum press ,NY,1984 Regards, Naitik N. Kothari "Animesh Sharma" 11/07/2001 09:00:53 AM GMT Please respond to bio_bulletin_board at bioinformatics.org |-----------------------------------------------------------+------------------| | |Return Receipt: No| | To: bio_bulletin_board at bioinformatics.org |Importance: Normal| | cc: (bcc: Naitik KOTHARI/ia/socgen) | | | | | |-----------------------------------------------------------+------------------| SUBJECT: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #127 - 3 msgs hello to all the members of bulletin board, i just joined this community and i feel it is a good place to share views and tools :) . i m a student of bioinformatics in JNU, delhi and wud like to have some help on a good book on ALGORITHM used in bioinformatics like SmithWaterman , Chous-Fasmann etc... or any links which explain this . thanks alot in advance ani ********************************************************************** the answer lies in genome ********************************************************************** dr.animesh sharma bioinformatics centre JNU,Delhi ************************************************************************** To better serve our clients and business partners, all SG staff in Asia Pacific now have a unique internet email address structured as follows: firstname.lastname at sgib.com. We suggest that you note this new reference in your address book as soon as possible, however for your convenience the previous address will continue to operate for 6 months. This change of address does not apply to our asset management, private banking and futures subsidiaries. They will continue to use their current addresses. Have you checked our new corporate website at http://www.sgib.com ? ************************************************************************** The information contained herein is confidential and is intended solely for the addressee(s). It shall not be construed as a recommendation to buy or sell any security. Any unauthorized access, use, reproduction, disclosure or dissemination is prohibited. Neither SGIB nor any of its subsidiaries or affiliates shall assume any legal liability or responsibility for any incorrect, misleading or altered information contained herein. ************************************************************************** From cmdobson at ucalgary.ca Thu Nov 8 13:17:24 2001 From: cmdobson at ucalgary.ca (C. Melissa Dobson) Date: Thu, 08 Nov 2001 11:17:24 -0700 Subject: [BiO BB] Re. Courses in bioinformatics References: Message-ID: <3BEACC34.6400386D@ucalgary.ca> > For those of you interested - here is a Bioinformatics course available in Canada Canadian Bioinformatics Workshops (CBW) - 2002 ---------------------------------------------- The Canadian Bioinformatics Workshops are a program of the Canadian Genetic Diseases Network and the Biotechnology Human Resources Council of Canada. In their third year, these workshops have attracted post-graduate students from around the world. The workshops are listed below with more details being available at www.bioinformatics.ca. 2002 Workshop Series ------------------- Bioinformatics February 18 - March 2, Vancouver Proteomics April 29 - May 4, Windsor NCBI Toolkit May 6 - 18, Windsor Programming I July 15 - 27, Montreal Developing the Tools August 9 - 16, Edmonton Genomics October 28 - November 2, Montreal For more information or to apply, visit http://www.bioinformatics.ca/workshops.php > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Pratap.Kotala at ndsu.nodak.edu Fri Nov 9 13:46:12 2001 From: Pratap.Kotala at ndsu.nodak.edu (Pratap Kotala) Date: Fri, 9 Nov 2001 12:46:12 -0600 Subject: [BiO BB] "Alignment editor for Blast results" Message-ID: <200111091846.fA9Ik8f03283@smtp1.ndsu.nodak.edu> Hi all, I had been following this list-serv for sometime and I find it pretty valuable. I have been working to setup a alignment editor for blast outputs. I am trying to use JalView multiple alignment editor to output the blast results. I was wondering, had there been earlier attempts made in this regard or am I reinventing the wheel. Any comments or suggestions are welcome. Thx, Pratap Kotala From bsmcfall at hotmail.com Fri Nov 9 15:08:40 2001 From: bsmcfall at hotmail.com (Brad McFall) Date: Fri, 09 Nov 2001 15:08:40 -0500 Subject: [BiO BB] survey plus taxomomy combine agent Message-ID: There is a need it seems to me in BioInformatic economic progress to translate lists of species for conservation vs management vs legal obligations into practical ecological triangles representing yield values that would have found a structural (in addition to causal(correlational)) similar uniformness level of confidence in a topography of the histogeny contained AND the habitat functionality by behavior developed (in the sense of unfolding of the draftsman(techno-bio craft/subject of discussion on this board))together. A common survay and taxonomy agent as in the latest epistemology out of gbif implementation posts elsewhere can give this information to the craftsman of any country and the topography specialized Either from internal or external interfaces but contrary to other IT proposals the DTD will be in use for the largest "evolving" project and not simply an algorithm to include definition of names in the diagram management. I am sorry if you do not understand as how I write but these ideas will become clearer even if curators of museum data continue to interact with me as they have in the past. The complexity could be further reduced if allele and chromosome frequiences can be in the fact finding founded on the same structure discovery (in addition to Any correlation or causation philosphized in) through Some traditional data (morphology/anatomy, chemistry contained, behavior observed, nomeclature in use, higher classification supported) and ALL organization level relevant (no matter any hypothetical selection) molecular bioinformatics. Thanks for being there. As I read the board the lingo will become more comprehensible. I am for a sustainable future. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From indraneel at indialine.org Tue Nov 13 17:23:39 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 13 Nov 2001 16:23:39 -0600 Subject: [BiO BB] Good OOP and Java Book In-Reply-To: References: Message-ID: <20011113162339.B13702@indialine.org> One of the ways is probably to learn C++. A working knowledge takes a month considering that you already know C. Maybe ADA is preferable though. Python is also relatively easy. OReilly books: Practical C++ programming Programming Python "Learning Java" looks like a good book but I have just browsed it once. \Indraneel On Tue, Nov 06, 2001 at 01:56:47PM +0000, Tanya Vavouri wrote: > Hi, > > I am starting a bioinformatics project in which I'll develop a program in > Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am > looking for a good book that will introduce me to OOP and then teach me > Java. Are there any books that you would recommend ? I have found some > titles but I'd like to have some opinions as well. -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Tue Nov 13 17:35:54 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 13 Nov 2001 16:35:54 -0600 Subject: [BiO BB] Unix or Linux In-Reply-To: <20011106173747.84595.qmail@web14506.mail.yahoo.com> References: <20011106173747.84595.qmail@web14506.mail.yahoo.com> Message-ID: <20011113163554.C13702@indialine.org> My desktop/laptop/servers (cluster -- coming soon!) all have debian scrawled on their screens. GNU/Linux is here to stay Hip, Hip, hurray! \Indraneel PS: Our supplier will be delivering AthlonXP as he ran out of Thunderbirds. Now, aint that just perfect timing? On Tue, Nov 06, 2001 at 09:37:46AM -0800, Peri Suraj wrote: > > 1. UNIX ( Digital, Solaris, IRIX that are proprietory > and robust) > 2. LINUX( Free, widely used and flexible) > > Folks, what would you prefer? -- http://www.indialine.org/indraneel/ From whatifwhatnext at on.aibn.com Tue Nov 13 18:05:24 2001 From: whatifwhatnext at on.aibn.com (Howard Oliver) Date: Tue, 13 Nov 2001 18:05:24 -0500 Subject: [BiO BB] Unix or Linux In-Reply-To: <20011113163554.C13702@indialine.org> Message-ID: HI. We would like to test the following marketing message. Would appreciate your comments Thanks Howard Oliver, Principal What If What Next Consulting holiver at whatifwhatnext.com www.whatifwhatnext.com ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ What If What Next(TM) Consulting provides rapid, results-driven business development services to leading edge technology companies. Our Typical Projects: ? Conduct business development projects including identifying, negotiating, drafting and closing deals that are aligned with the client's goals ? Develop international alliances ? Assume Business Development functions for 6 ?12 months achieving predefined targets and infrastructure We have an interest in working with Bioinformatics and IT firms who are serving the life sciences sector and who wish to have a business development resource located in Toronto, Canada. We have created a set of scenarios on Post-Genomic Bioinformatics that we would be pleased to send to you. It is a good first step to understanding our approach and explore how we can help you enhance your business development program in North America. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From hzi at uol.com.br Tue Nov 13 19:46:03 2001 From: hzi at uol.com.br (hzi at uol.com.br) Date: Tue, 13 Nov 2001 22:46:03 -0200 Subject: [BiO BB] Unix or Linux In-Reply-To: <20011113163554.C13702@indialine.org>; from indraneel@indialine.org on Tue, Nov 13, 2001 at 04:35:54PM -0600 References: <20011106173747.84595.qmail@web14506.mail.yahoo.com> <20011113163554.C13702@indialine.org> Message-ID: <20011113224603.B2676@siddhi.uol.com.br> On Tue, Nov 13, 2001 at 04:35:54PM -0600, Indraneel Majumdar wrote: > My desktop/laptop/servers (cluster -- coming soon!) all have debian > scrawled on their screens. > > GNU/Linux is here to stay > Hip, Hip, hurray! > > \Indraneel > > PS: Our supplier will be delivering AthlonXP as he ran out of > Thunderbirds. Now, aint that just perfect timing? > > On Tue, Nov 06, 2001 at 09:37:46AM -0800, Peri Suraj wrote: > > > > 1. UNIX ( Digital, Solaris, IRIX that are proprietory > > and robust) > > 2. LINUX( Free, widely used and flexible) > > > > Folks, what would you prefer? > I've never used Unix. In terms of Linux, I've tried RedHat and Conectiva, but I know use Debian. It's very easy to update your system with it. You can download 100Mb of software and, when it's done, you just press and it will install withou a flaw. Much better that the rpm system, where you keep getting those "ooops, there's a package missing here!" messages. From what I read there's a general trend to substitute Unix for Linux (I read this in the specialized press). Give Debian GNU/Linux a try. You won't regret it. Regards, Henry From biologynext at yahoo.com Tue Nov 13 22:19:28 2001 From: biologynext at yahoo.com (Bio Next) Date: Tue, 13 Nov 2001 19:19:28 -0800 (PST) Subject: [BiO BB] Good OOP and Java Book In-Reply-To: <20011113162339.B13702@indialine.org> Message-ID: <20011114031928.29809.qmail@web21107.mail.yahoo.com> Hi Tanya: One of the best books for learning Java concepts, programmings and tricks is 'Thinking in Java' by Bruce Eckel. You can learn Object Oriented Design concepts as well. The book is free and the 2nd edition can be downloaded 'free' from: http://www.mindview.net/Books/TIJ/ Additionally if you are really serious about OOAD and how it is best applied when programming using Java language, please take a look at 'Java Design' by Peter Coad et' al. Hope this helps. -BiologyNext. > On Tue, Nov 06, 2001 at 01:56:47PM +0000, Tanya Vavouri wrote: > > Hi, > > > > I am starting a bioinformatics project in which I'll develop a > program in > > Java. Since I have no experience in Java and OOP (only C/Perl/VB) I > am > > looking for a good book that will introduce me to OOP and then > teach me > > Java. Are there any books that you would recommend ? I have found > some > > titles but I'd like to have some opinions as well. > __________________________________________________ Do You Yahoo!? Find the one for you at Yahoo! Personals http://personals.yahoo.com From biologynext at yahoo.com Tue Nov 13 22:24:52 2001 From: biologynext at yahoo.com (Bio Next) Date: Tue, 13 Nov 2001 19:24:52 -0800 (PST) Subject: [BiO BB] Unix or Linux In-Reply-To: <20011113163554.C13702@indialine.org> Message-ID: <20011114032452.82776.qmail@web21105.mail.yahoo.com> Hi: The ends must justify the means. 1. If you are prudent with budget and primarily focus on number crunching then use Linux ( preferably RedHat 7.1 ). The I/O capabilities in Linux beat the other UNices pants down and is even faster than Windows, though marginally. 2. If you are more interested in analysis of information in a visually intuitive way, invest in Windows NT ( SP 6 ) so that you a sophisticated and mature UI. Avoid Win9X and Win2K and WinXP because they are either not stable or just demanding in terms of hardware requirements. However NT Server 4.0 is currently quite stable and doesn't crash at all, if you have been careful with the quality of RAM. Let me know if you need additional quantitative data. Hope this helps. -BiologyNext. > On Tue, Nov 06, 2001 at 09:37:46AM -0800, Peri Suraj wrote: > > > > 1. UNIX ( Digital, Solaris, IRIX that are proprietory > > and robust) > > 2. LINUX( Free, widely used and flexible) > > > > Folks, what would you prefer? > __________________________________________________ Do You Yahoo!? Find the one for you at Yahoo! Personals http://personals.yahoo.com From biologynext at yahoo.com Tue Nov 13 22:26:39 2001 From: biologynext at yahoo.com (Bio Next) Date: Tue, 13 Nov 2001 19:26:39 -0800 (PST) Subject: [BiO BB] Marketing message In-Reply-To: Message-ID: <20011114032639.17647.qmail@web21101.mail.yahoo.com> Sounds good! --- Howard Oliver wrote: > > HI. > > We would like to test the following marketing message. Would > appreciate your > comments > > Thanks > > Howard Oliver, Principal What If What Next Consulting > holiver at whatifwhatnext.com www.whatifwhatnext.com > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > What If What Next(TM) Consulting provides rapid, results-driven > business > development services to leading edge technology companies. > > Our Typical Projects: > ? Conduct business development projects including identifying, > negotiating, > drafting and closing deals that are aligned with the client's goals > ? Develop international alliances > ? Assume Business Development functions for 6 ?12 months achieving > predefined targets and infrastructure > > We have an interest in working with Bioinformatics and IT firms who > are > serving the life sciences sector and who wish to have a business > development > resource located in Toronto, Canada. > > We have created a set of scenarios on Post-Genomic Bioinformatics > that we > would be pleased to send to you. It is a good first step to > understanding > our approach and explore how we can help you enhance your business > development program in North America. > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > __________________________________________________ Do You Yahoo!? Find the one for you at Yahoo! Personals http://personals.yahoo.com From Joel.Dudley at DevelopOnline.com Wed Nov 14 10:04:56 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 14 Nov 2001 08:04:56 -0700 Subject: [BiO BB] Unix or Linux Message-ID: NT Server 4.0 is quite stable and does not crash at all?? On what planet??? -----Original Message----- From: Bio Next [mailto:biologynext at yahoo.com] Sent: Tuesday, November 13, 2001 8:25 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Unix or Linux Hi: The ends must justify the means. 1. If you are prudent with budget and primarily focus on number crunching then use Linux ( preferably RedHat 7.1 ). The I/O capabilities in Linux beat the other UNices pants down and is even faster than Windows, though marginally. 2. If you are more interested in analysis of information in a visually intuitive way, invest in Windows NT ( SP 6 ) so that you a sophisticated and mature UI. Avoid Win9X and Win2K and WinXP because they are either not stable or just demanding in terms of hardware requirements. However NT Server 4.0 is currently quite stable and doesn't crash at all, if you have been careful with the quality of RAM. Let me know if you need additional quantitative data. Hope this helps. -BiologyNext. > On Tue, Nov 06, 2001 at 09:37:46AM -0800, Peri Suraj wrote: > > > > 1. UNIX ( Digital, Solaris, IRIX that are proprietory > > and robust) > > 2. LINUX( Free, widely used and flexible) > > > > Folks, what would you prefer? > __________________________________________________ Do You Yahoo!? Find the one for you at Yahoo! Personals http://personals.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From biologynext at yahoo.com Wed Nov 14 22:39:47 2001 From: biologynext at yahoo.com (Bio Next) Date: Wed, 14 Nov 2001 19:39:47 -0800 (PST) Subject: [BiO BB] RE: NT Server stability In-Reply-To: Message-ID: <20011115033947.70599.qmail@web21107.mail.yahoo.com> Hi Joel: NT 4.0 Server is comparatively quite stable since there have been quite a few service packs ( 7 to be precise ). The stability is compared to the other OSes that have been shipped from MSFT stable. My point was that if the user plans to invest in UI intensive tools esp. for visualization / modeling etc then it is more cost effective to have a NT box. I would always try to recommend a solution from the perspective of effectiveness in a given scenario rather than some religious incantation. Have a nice day! -BN. --- Joel Dudley wrote: > NT Server 4.0 is quite stable and does not crash at all?? On what > planet??? > > -----Original Message----- > From: Bio Next [mailto:biologynext at yahoo.com] > Sent: Tuesday, November 13, 2001 8:25 PM > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Unix or Linux > > > > Hi: > > 2. If you are more interested in analysis of information in a > visually intuitive way, invest in Windows NT ( SP 6 ) so that > you a sophisticated and mature UI. > Avoid Win9X and Win2K and WinXP because they are either not > stable or just demanding in terms of hardware requirements. > However NT Server 4.0 is currently quite stable and doesn't > crash at all, if you have been careful with the quality of RAM. > __________________________________________________ Do You Yahoo!? Find the one for you at Yahoo! Personals http://personals.yahoo.com From jeff at bioinformatics.org Wed Nov 14 23:48:18 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 14 Nov 2001 23:48:18 -0500 Subject: [BiO BB] [Fwd: From journalist in New Delhi, India] Message-ID: <3BF34912.EEF545E6@bioinformatics.org> I thought that the BBB subscribers might be able to answer these questions, particularly those from India. Note that this person is not on the mailing list, so CC to . Jeff -------------- next part -------------- An embedded message was scrubbed... From: "Nivedita Mookerji" Subject: From journalist in New Delhi, India Date: Thu, 15 Nov 2001 00:20:53 +0530 Size: 6543 URL: From hzi at uol.com.br Thu Nov 15 19:39:16 2001 From: hzi at uol.com.br (hzi at uol.com.br) Date: Thu, 15 Nov 2001 22:39:16 -0200 Subject: [BiO BB] RE: NT Server stability In-Reply-To: <20011115033947.70599.qmail@web21107.mail.yahoo.com>; from biologynext@yahoo.com on Wed, Nov 14, 2001 at 07:39:47PM -0800 References: <20011115033947.70599.qmail@web21107.mail.yahoo.com> Message-ID: <20011115223916.F21381@siddhi.uol.com.br> On Wed, Nov 14, 2001 at 07:39:47PM -0800, Bio Next wrote: > > Hi Joel: > > My point was that if the user plans to invest in UI intensive > tools esp. for visualization / modeling etc then it is more > cost effective to have a NT box. > How do you mean? Do you mean there's less free software in this area (vis/mod)? > I would always try to recommend a solution from the perspective > of effectiveness in a given scenario rather than some religious > incantation. Define the scenario, please. Can you give real world examples? On religion incantations: Let's not get into this. The day NASA chooses Windows I will too. And why is it every computer tomographer I see has a Tk interface? And, oh remember politics of free software and genome data? > Have a nice day! > > -BN. Regards, HL From diwali-greetings at indogram.net Thu Nov 15 19:04:58 2001 From: diwali-greetings at indogram.net (diwali-greetings at indogram.net) Date: Thu, 15 Nov 2001 16:04:58 -0800 (PST) Subject: [BiO BB] Happy Diwali! Message-ID: <1903006.1005873592550.JavaMail.vijayan@julion> An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Thu Nov 15 21:18:48 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 15 Nov 2001 21:18:48 -0500 Subject: [BiO BB] about moderation Message-ID: <3BF47788.11460B5D@bioinformatics.org> It appears that the first SPAM message has made it through the filter. Up until now, we haven't been moderating the forum, but if the SPAM (or trolling) gets heavy, we'll do that. Usually the SPAM diminishes after a while, so we'll take the wait-and-see approach. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From bioinfo_india at yahoo.com Fri Nov 16 04:19:30 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Fri, 16 Nov 2001 01:19:30 -0800 (PST) Subject: [BiO BB] about moderation In-Reply-To: <3BF47788.11460B5D@bioinformatics.org> Message-ID: <20011116091930.68451.qmail@web14510.mail.yahoo.com> hi Jeff, you are right. Its good to take measures to avoid spamers. but does this moderation leads to delay in posting? whats your opinion. cheers sp ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Find the one for you at Yahoo! Personals http://personals.yahoo.com From jeff at bioinformatics.org Mon Nov 19 10:48:32 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 19 Nov 2001 10:48:32 -0500 Subject: [BiO BB] about moderation References: <20011116091930.68451.qmail@web14510.mail.yahoo.com> Message-ID: <3BF929D0.195C070D@bioinformatics.org> Peri Suraj wrote: > > you are right. Its good to take measures to avoid > spamers. but does this moderation leads to delay in > posting? > whats your opinion. I had problems with spammers on some of the other lists that I've managed. When filtering failed, I tried restricting posts to members only, and I also tried holding posts for approval. Neither approach was greeted very well by subscribers, who commented that they'd rather put up with a few SPAMs than restricted or delayed posts. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From bioinformaticsckk at yahoo.co.in Mon Nov 19 04:51:24 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Mon, 19 Nov 2001 09:51:24 +0000 (GMT) Subject: [BiO BB] from kiran kumar Message-ID: <20011119095124.85965.qmail@web8005.mail.in.yahoo.com> Hello everyone, I am working with eukaryotic promoter analysis. could anyone explain me how exon1 of eukaryotic genes could be characterised or annotated by wet lab experiments. I mean how experimentally exon1 can be proved of a given sequence. Thank you in advance. Kiran kumar ____________________________________________________________ *NEW* over 2200 active jobs at Yahoo! Careers *NEW* Visit http://in.careers.yahoo.com/ From tendo at crick.mri.tmd.ac.jp Mon Nov 19 22:09:22 2001 From: tendo at crick.mri.tmd.ac.jp (Toshinori Endo) Date: Tue, 20 Nov 2001 12:09:22 +0900 Subject: [BiO BB] from kiran kumar In-Reply-To: <20011119095124.85965.qmail@web8005.mail.in.yahoo.com> Message-ID: Hi kiran, Here is the abstract of the method todetermine the exon 1, which you can find the detailed description in a standard textbook like molecular biology of the gene or a cook book like molecular cloning. There are severals ways to confirm the exon 1. First is to compare the sequence with the 5' end of cDNA or mRNA by in silico comparison or by hybridization. Second is to determine whether or not it is the true end, S1 mapping may be performed, which is based on the hybridization between genomic DNA and messenger RNA followed by the digestion of single stranded RNA by S1 RNase. This method can be applied to determine splice sites as well as 3' end. Another method may also be employed, that is primer extension. The third is to perform in vitro transcription to compare the size of spliced form of the transcript with that of mRNA by electrophoresis which ensures the there are no missing fragment in the genomic clone. They may sometime perfom in vitro tranlation as well. If they have isolated protein sample which is relatively rare case in the recent study, they compare the molecular weight of translated product with native protein. Otherwise, they may obtain the antibody somehow, so that they can compare the MW of experimentally obtained protein with that of native one. Those information will not appear in GenBank annotation. You can find them only in literatures. In addition, not many researchers cares whether or not they have true 5' end as long as the have sequence contain whole coding sequence, which may be comfirmed by in vitro translation described above. Note that exon 1 does not necessary code the initiation codon. That is, it may contain just a 5'UTR of the gene. In such a case, coding sequence starts in the second exon or even in the third. Toshinori Endo > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of > kiran challapalli > Sent: Monday, November 19, 2001 6:51 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] from kiran kumar > > > Hello everyone, > I am working with eukaryotic promoter analysis. could > anyone explain me how exon1 of eukaryotic genes could > be characterised or annotated by wet lab experiments. > I mean how experimentally exon1 can be proved of a > given sequence. > Thank you in advance. > Kiran kumar > > ____________________________________________________________ > *NEW* over 2200 active jobs at Yahoo! Careers *NEW* > Visit http://in.careers.yahoo.com/ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From bioinfo_india at yahoo.com Tue Nov 20 02:58:51 2001 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Mon, 19 Nov 2001 23:58:51 -0800 (PST) Subject: [BiO BB] from kiran kumar In-Reply-To: Message-ID: <20011120075851.59352.qmail@web14510.mail.yahoo.com> Hi, Toshinori very well explained various methods and ideas to deal with characterization of end exons. As he said, Exon I can be a a non-coiding exon in the a given gene. And thus its a part of 5'UTR. Traditional cDNA libraries yield, many times incomplete ends of the cDNA. In such cases one can either perform 5'RACE or 3'RACE to extend 5' or 3' ends respectively. But in present day setup many labs prefer to do insilico analysis and confirm the completeness of a given gene based on ESTs. SP ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From bioash at hotmail.com Tue Nov 20 12:52:08 2001 From: bioash at hotmail.com (Ashwin Sivakumar) Date: Tue, 20 Nov 2001 17:52:08 +0000 Subject: [BiO BB] splice signals prediction? Message-ID: An HTML attachment was scrubbed... URL: From hzi at uol.com.br Tue Nov 20 19:06:08 2001 From: hzi at uol.com.br (hzi at uol.com.br) Date: Tue, 20 Nov 2001 22:06:08 -0200 Subject: [BiO BB] Has anyone ever tried Lisp? Message-ID: <20011120220608.B3035@siddhi.uol.com.br> Hi- Just out of curiosity: I was looking at Lisp, and found it to be pretty interesting. Lispers claim is can really __scale__. Has anyone tried Lisp at all here? Anything done on bioinfo with Lisp? I dopn't know, the more I look into Lisp, the more tempted I am...How about you? Check out: Regards, -HL From hzi at uol.com.br Tue Nov 20 19:02:20 2001 From: hzi at uol.com.br (hzi at uol.com.br) Date: Tue, 20 Nov 2001 22:02:20 -0200 Subject: [BiO BB] Good OOP and Java Book In-Reply-To: <20011113162339.B13702@indialine.org>; from indraneel@indialine.org on Tue, Nov 13, 2001 at 04:23:39PM -0600 References: <20011113162339.B13702@indialine.org> Message-ID: <20011120220220.A3035@siddhi.uol.com.br> > > On Tue, Nov 06, 2001 at 01:56:47PM +0000, Tanya Vavouri wrote: > > Hi, > > > > I am starting a bioinformatics project in which I'll develop a program in > > Java. Since I have no experience in Java and OOP (only C/Perl/VB) I am > > looking for a good book that will introduce me to OOP and then teach me > > Java. Are there any books that you would recommend ? I have found some > > titles but I'd like to have some opinions as well. > May I suggest that you try the language Ruby? Ruby, unlike other languages cited in this thread (not that they're not good languages), is 100% object-oriented. __Everything__ in Ruby is an object. It really makes you think __differently__ (in terms of OOP; other paradigms exists, eg, functional programming languages, like Haskell.) Regards, -HL From muppetman559 at hotmail.com Wed Nov 21 01:10:34 2001 From: muppetman559 at hotmail.com (James Thompson) Date: Wed, 21 Nov 2001 00:10:34 -0600 Subject: [BiO BB] Has anyone ever tried Lisp? Message-ID: I've heard people say that Lisp should be something that any programmer learns, regardless of whether they ever use it again or not, because of they way it teaches you to think. My most recent programming classes used Scheme, which is a dialect of Lisp. I really liked it, it forced me to think in a much more abstract way than most other computer science courses that I've ever taken, and I think that this has helped the way in which I will design and implement programs in the future. Iit allowed some extremely graceful solutions to problems that we were given in class. I definitely think that it is worth checking out. Here are some links for those who interested: Paul Graham used LISP to design a program that was eventually bought by Yahoo and become Yahoo Stores, here is his article on the subject: http://www.paulgraham.com/avg.html Endpoint Computer is a company that uses LISP to help solve a variety of problems, here is their rational for it: http://www.endpointcomputing.com/articles/lisp.html One of the more interesting articles that I've read concerns the use of Lisp as a Java Alternative: http://www-aig.jpl.nasa.gov/public/home/gat/lisp-study.html Happy Lisping everyone, and I wish you all a good Thanksgiving. James Thompson _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From HurtDP at appliedbiosystems.com Wed Nov 21 04:00:10 2001 From: HurtDP at appliedbiosystems.com (HurtDP at appliedbiosystems.com) Date: Wed, 21 Nov 2001 01:00:10 -0800 Subject: [BiO BB] David P Hurt is out of the office. Message-ID: I will be out of the office starting 11/20/2001 and will not return until 11/27/2001. Regards David Hurt From jwester at sgi1.chemie.uni-hamburg.de Wed Nov 21 08:04:19 2001 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Wed, 21 Nov 2001 14:04:19 +0100 Subject: [BiO BB] Has anyone ever tried Lisp? References: <20011120220608.B3035@siddhi.uol.com.br> Message-ID: <3BFBA653.B975AE20@sgi1.chemie.uni-hamburg.de> hzi at uol.com.br wrote: > Has anyone tried Lisp at all here? Anything done on bioinfo > with Lisp? Bioinformatics can be done with any kind of language. Some are more usefull for certain problems. LISP is often used in Artificial Intelligence (AI) and related methods like neural networks or genetic algorithms. These are often used in bioinfo or QSAR/QSPR studies. jcw -- Jan-C. Westermann jwester at sgi1.chemie.uni-hamburg.de Nota bene: wenn Word f?r L?ngeres geeignet w?re, w?rde es schlie?lich nicht Word, sondern Sentence, Page oder Article hei?en ;-) Matthias M?hlich in dctt From jim at gellman.net Wed Nov 21 10:55:42 2001 From: jim at gellman.net (jim gellman) Date: Wed, 21 Nov 2001 07:55:42 -0800 Subject: [BiO BB] Has anyone ever tried Lisp? In-Reply-To: <20011120220608.B3035@siddhi.uol.com.br> Message-ID: <001e01c172a4$fbdc3400$4e899dd1@gellman.net> Lisp, and the related dialect Scheme, are both fun languages to work with, and I agree that you can learn a lot about programming through them. In particular, the Scheme book "The Structure and Interpretation of Computer Programs" by Abelson and Sussman is an excellent book that will challenge the way you think about programming and deepen your enthusiasm for the craft. Whether or not it will scale, though, depends on what you mean by the word. I'd hesitate to use either for a large, multi-person project because of the lack of a type system. Proper use of types can prevent a whole lot of errors as software components evolve in large and small ways, and engineers come and go. jim > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of > hzi at uol.com.br > Sent: Tuesday, November 20, 2001 4:06 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Has anyone ever tried Lisp? > > > Hi- > > Just out of curiosity: I was looking at Lisp, and found it to > be pretty interesting. Lispers claim is can really __scale__. > > Has anyone tried Lisp at all here? Anything done on bioinfo > with Lisp? > I dopn't know, the more I look into Lisp, the more tempted I > am...How about you? > > Check out: > > Regards, > -HL > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From malcook at san.rr.com Wed Nov 21 14:43:07 2001 From: malcook at san.rr.com (Malcolm Cook) Date: Wed, 21 Nov 2001 11:43:07 -0800 Subject: [BiO BB] Has anyone ever tried Lisp? In-Reply-To: <001e01c172a4$fbdc3400$4e899dd1@gellman.net> Message-ID: <000801c172c4$be1b4820$020110ac@san.rr.com> Some BioInf work on at SRI Take a look at www.biolisp.org - offerings pretty thin but there is some activity... -Malcolm Cook > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of jim > gellman > Sent: Wednesday, November 21, 2001 7:56 AM > To: bio_bulletin_board at bioinformatics.org > Subject: RE: [BiO BB] Has anyone ever tried Lisp? > > > Lisp, and the related dialect Scheme, are both fun languages to work with, > and I agree that you can learn a lot about programming through them. In > particular, the Scheme book "The Structure and Interpretation of Computer > Programs" by Abelson and Sussman is an excellent book that will challenge > the way you think about programming and deepen your enthusiasm for the > craft. > > Whether or not it will scale, though, depends on what you mean by > the word. > I'd hesitate to use either for a large, multi-person project > because of the > lack of a type system. Proper use of types can prevent a whole lot of > errors as software components evolve in large and small ways, and > engineers > come and go. > > jim > > > -----Original Message----- > > From: bio_bulletin_board-admin at bioinformatics.org > > [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of > > hzi at uol.com.br > > Sent: Tuesday, November 20, 2001 4:06 PM > > To: bio_bulletin_board at bioinformatics.org > > Subject: [BiO BB] Has anyone ever tried Lisp? > > > > > > Hi- > > > > Just out of curiosity: I was looking at Lisp, and found it to > > be pretty interesting. Lispers claim is can really __scale__. > > > > Has anyone tried Lisp at all here? Anything done on bioinfo > > with Lisp? > > I dopn't know, the more I look into Lisp, the more tempted I > > am...How about you? > > > > Check out: > > > > Regards, > > -HL > > > > > > > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From whatifwhatnext at on.aibn.com Wed Nov 21 14:57:51 2001 From: whatifwhatnext at on.aibn.com (Howard Oliver) Date: Wed, 21 Nov 2001 14:57:51 -0500 Subject: [BiO BB] Question In-Reply-To: <000801c172c4$be1b4820$020110ac@san.rr.com> Message-ID: Hi: Im doing some research on Bioinformatics applications that require the manipulation of very large databases of terabyte size and beyond. Any suggestions? Howard From Joel.Dudley at DevelopOnline.com Wed Nov 21 17:24:59 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 21 Nov 2001 15:24:59 -0700 Subject: [BiO BB] Question Message-ID: If you look at Postgresql (www.postgresql.org) you will see it can handle data loads of that proportion. - Joel -----Original Message----- From: Howard Oliver To: bio_bulletin_board at bioinformatics.org Sent: 11/21/01 12:57 PM Subject: [BiO BB] Question Hi: Im doing some research on Bioinformatics applications that require the manipulation of very large databases of terabyte size and beyond. Any suggestions? Howard _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From danag at bioinformatics.weizmann.ac.il Sun Nov 25 10:59:31 2001 From: danag at bioinformatics.weizmann.ac.il (Dana Gerber) Date: Sun, 25 Nov 2001 17:59:31 +0200 Subject: [BiO BB] alternative splicing Message-ID: <3C011561.B6B0F227@bioinfo.weizmann.ac.il> Hi, Does anyone know about some methods for alternative splicing prediction. I know only about prediction methods that are based on ESTs? Are there other approaches? Thanks a lot, Dana From rworthin at watson.wustl.edu Sun Nov 25 11:21:55 2001 From: rworthin at watson.wustl.edu (Ron Worthington, Ph.D.) Date: Sun, 25 Nov 2001 10:21:55 -0600 Subject: [BiO BB] alternative splicing References: <3C011561.B6B0F227@bioinfo.weizmann.ac.il> Message-ID: <3C011A9E.D143D041@watson.wustl.edu> Hi, Both of the programs Genscan (Burge) and HMMgene (Krogh) report suboptimal exon structures, and these suboptimal exons can be tested as possible alternative splicing forms. -Ron Dana Gerber wrote: > Hi, > > Does anyone know about some methods for alternative splicing > prediction. I know only about prediction methods that are based on > ESTs? Are there other approaches? > > Thanks a lot, > Dana > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From danag at bioinformatics.weizmann.ac.il Tue Nov 27 07:47:59 2001 From: danag at bioinformatics.weizmann.ac.il (Dana Gerber) Date: Tue, 27 Nov 2001 14:47:59 +0200 Subject: [BiO BB] expression profile Message-ID: <3C038B79.A0ECFA2F@bioinfo.weizmann.ac.il> Hi, Where can I find a expression profile of specific gene from c.elegans, mouse and E.coli. I need any information about their lethality, tissue specific expression, condition specific expression. It's unknown gene that don't have any information in central database such as WormDB, AceDB, EcoCyc and others. Thanks a lot, all best, Dana From mucastic at yahoo.com Tue Nov 27 14:02:01 2001 From: mucastic at yahoo.com (Harini Kumar) Date: Tue, 27 Nov 2001 11:02:01 -0800 (PST) Subject: [BiO BB] Genetic algorithms In-Reply-To: <3C038B79.A0ECFA2F@bioinfo.weizmann.ac.il> Message-ID: <20011127190201.91835.qmail@web13802.mail.yahoo.com> hi, i am a bachelor of engg. student. I have a very hazy knowledge on assorted topics concerning bioinformatics and genetic algorithms. I'd like to learn the basics of genetic algorithms..the 'very' basics! Can anyone suggest any authored book on this subject. sincerely, M. __________________________________________________ Do You Yahoo!? Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From Manoj_Kenkare at frost.com Tue Nov 27 14:30:07 2001 From: Manoj_Kenkare at frost.com (Manoj Kenkare) Date: Tue, 27 Nov 2001 13:30:07 -0600 Subject: [BiO BB] Bioinformatics & Drug Discovery Message-ID: Frost & Sullivan is an international Marketing Consulting & Training Company. Our Drug Discovery Subscription offers different reports and research in the area of Drug Discovery Technologies and Genomics. As a part of the subscription Frost & Sullivan plans to provide 20 deliverables during 2001 and 2002. Besides the 20 deliverables subscribers will also have access to atleast 4 updates on the industry and technology trends. Some of the upcoming deliverables within the Proteomics Subscription are: Report # Region Existing Deliverables 7744-55 US Bioinformatics A110-53 US Challenges and Threats from Bioterrorism 7801-55 US High Throughput Screening 7965-55 US Pharmacogenomics 7761-55 WD World Biochip Market 7246-55 WD Introduction to the World SNP Detection Technology Market 5822-55 WD Proteomics 8118-52 PA PharmAsia - Bioinformatics in Singapore 5820-55 WD Opportunities for DNA Microchip and Array Technologies 5821-55 US Combinatorial Chemistry 5728-55 US Biotech & Pharmaceutical Analytical Instrument 3743-53 EU Biotechnology Based Diagnostics 5847-53 US DNA/RNA Probes 5407-55 US Neurogenomics 5837-70 US Bioinformatics in the Emerging Drug Discovery Marketplace 5723-55 US Opportunities in Genomics and the Associated HTS Mkts You will also have access to world class analysts working in this area and free access to analyst briefings conducted by Frost & Sullivan. Subscribers will also have access to industry news and analyst insights through our Biotech & Drug Discovery Portal that was released recently. As a valued client and an industry leader Frost & Sullivan would like to provide you with a Free copy of the one of the best selling report: Proteomics Profiles (Report #6390 published 2001) if you sign-up for the Drug Discovery subscription before December 10,2001. If you have already bought a copy of this report Frost & Sullivan will write-off the purchase price of this report from the subscription price of the Proteomics Subscription. We encourage you to seize this opportunity and subscribe to our service before the December 10,2001. To sign-up please call our Biotech/DDT Sales at 210-247-2443 or write to us at mkenkare at frost.com with your contact information and questions. -------------- next part -------------- An HTML attachment was scrubbed... URL: From RMayreddy at NBME.org Tue Nov 27 16:09:19 2001 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Tue, 27 Nov 2001 16:09:19 -0500 Subject: [BiO BB] Bioinformatics & Drug Discovery Message-ID: Workshop on Bioinformatics _____ PERL AND BIOPERL FOR BIOINFORMATICS (BIT- 01) Three Days Workshop Schedule: Day One (December 01, 2001) 09:00 Registration and Breakfast 09:30 - 12:30 PERL: syntax, semantics and applications 12:30 - 01:30 Lunch 01:30 - 03:30 PERL: Hands on training 03:30 - 04:00 Breakout session Day Two (December 08, 2001) 09:00 Breakfast 09:30 - 12:30 PERL: review of Perl scripts, practice and projects 12:30 - 01:30 Lunch 01:30 - 03:30 BIOPERL: Object oriented approach and web resources 03:30 - 04:00 Breakout session Day Three (December 15, 2001) 09:00 Breakfast 09:30 - 12:30 BIOPERL: modules, methods and interfaces 12:30 - 01:30 Lunch 01:30 - 03:30 BIOPERL: Case studies BioPerl in analyzing inheritable disorders 03:30 - 03:35 Announcements of collaborative projects 03:35 - 04:00 Breakout session Place: Temple University Center City Campus (TUCC) 1515 Market Street, Philadelphia, PA 19102 (right at the Subway exit) Parking: Free (Only at PARK & LOCK)Entrance through 16th St., between Chestnut St. & Market St., on the right side. To get free parking - You must bring your parking ticket to the Registration table. Fee: Complete Module (Three days program) i. $500 for participants from academics ii. $750 for participants from industry Daily Workshop (Each of above three days) i. $200 for participants from academics $300 for participants from industries Contact: (267) 254-2075 / ssi-informatics at shikara-systems.com -----Original Message----- From: Manoj Kenkare [mailto:Manoj_Kenkare at frost.com] Sent: Tuesday, November 27, 2001 2:30 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Bioinformatics & Drug Discovery Frost & Sullivan is an international Marketing Consulting & Training Company. Our Drug Discovery Subscription offers different reports and research in the area of Drug Discovery Technologies and Genomics. As a part of the subscription Frost & Sullivan plans to provide 20 deliverables during 2001 and 2002. Besides the 20 deliverables subscribers will also have access to atleast 4 updates on the industry and technology trends. Some of the upcoming deliverables within the Proteomics Subscription are: Report # Region Existing Deliverables 7744-55 US Bioinformatics A110-53 US Challenges and Threats from Bioterrorism 7801-55 US High Throughput Screening 7965-55 US Pharmacogenomics 7761-55 WD World Biochip Market 7246-55 WD Introduction to the World SNP Detection Technology Market 5822-55 WD Proteomics 8118-52 PA PharmAsia - Bioinformatics in Singapore 5820-55 WD Opportunities for DNA Microchip and Array Technologies 5821-55 US Combinatorial Chemistry 5728-55 US Biotech & Pharmaceutical Analytical Instrument 3743-53 EU Biotechnology Based Diagnostics 5847-53 US DNA/RNA Probes 5407-55 US Neurogenomics 5837-70 US Bioinformatics in the Emerging Drug Discovery Marketplace 5723-55 US Opportunities in Genomics and the Associated HTS Mkts You will also have access to world class analysts working in this area and free access to analyst briefings conducted by Frost & Sullivan. Subscribers will also have access to industry news and analyst insights through our Biotech & Drug Discovery Portal that was released recently. As a valued client and an industry leader Frost & Sullivan would like to provide you with a Free copy of the one of the best selling report: Proteomics Profiles (Report #6390 published 2001) if you sign-up for the Drug Discovery subscription before December 10,2001. If you have already bought a copy of this report Frost & Sullivan will write-off the purchase price of this report from the subscription price of the Proteomics Subscription. We encourage you to seize this opportunity and subscribe to our service before the December 10,2001. To sign-up please call our Biotech/DDT Sales at 210-247-2443 or write to us at mkenkare at frost.com with your contact information and questions. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tompoe at renonevada.net Tue Nov 27 23:00:40 2001 From: tompoe at renonevada.net (tom poe) Date: Tue, 27 Nov 2001 20:00:40 -0800 Subject: [BiO BB] government contract opps Message-ID: <01112720004001.10807@aether> Hi: Where would be an appropriate place to post for contract opps for government agencies? I have need of three (3) bioinformatics researchers for an upcoming government contract submission. In other words, where do you folks look, when you're looking? thanks, tom From jwester at sgi1.chemie.uni-hamburg.de Wed Nov 28 04:33:58 2001 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Wed, 28 Nov 2001 10:33:58 +0100 Subject: [BiO BB] Genetic algorithms References: <20011127190201.91835.qmail@web13802.mail.yahoo.com> Message-ID: <3C04AF86.1FFA652D@sgi1.chemie.uni-hamburg.de> Harini Kumar wrote: > > hi, > i am a bachelor of engg. student. > I have a very hazy knowledge on assorted topics > concerning bioinformatics and genetic algorithms. > I'd like to learn the basics of genetic > algorithms..the 'very' basics! > Can anyone suggest any authored book on this subject. Maybe: An Introduction to Genetic Algorithms M. Mitchell MIT Press 0-262-63185-7 jcw -- Jan-C. Westermann jwester at sgi1.chemie.uni-hamburg.de Nota bene: wenn Word f?r L?ngeres geeignet w?re, w?rde es schlie?lich nicht Word, sondern Sentence, Page oder Article hei?en ;-) Matthias M?hlich in dctt From whatifwhatnext at on.aibn.com Wed Nov 28 18:00:07 2001 From: whatifwhatnext at on.aibn.com (Howard Oliver) Date: Wed, 28 Nov 2001 18:00:07 -0500 Subject: [BiO BB] Genetic algorithms In-Reply-To: <3C04AF86.1FFA652D@sgi1.chemie.uni-hamburg.de> Message-ID: HI: Yes there is a book by Wiley called Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins by A Baxevans and BF Ouellette. We also have some basic information on our site. Good luck, Howard Oliver Principal What If What Next (TM) Consulting holiver at whatifwhatnext.com Tel: 416-638-8582 Mobile: 416-432-2764 www.whatifwhatnext.com -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Jan-Christoph Westermann Sent: Wednesday, November 28, 2001 4:34 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Genetic algorithms Harini Kumar wrote: > > hi, > i am a bachelor of engg. student. > I have a very hazy knowledge on assorted topics > concerning bioinformatics and genetic algorithms. > I'd like to learn the basics of genetic > algorithms..the 'very' basics! > Can anyone suggest any authored book on this subject. Maybe: An Introduction to Genetic Algorithms M. Mitchell MIT Press 0-262-63185-7 jcw -- Jan-C. Westermann jwester at sgi1.chemie.uni-hamburg.de Nota bene: wenn Word f?r L?ngeres geeignet w?re, w?rde es schlie?lich nicht Word, sondern Sentence, Page oder Article hei?en ;-) Matthias M?hlich in dctt _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: Howard Oliver (E-mail).vcf Type: text/x-vcard Size: 530 bytes Desc: not available URL: From RMayreddy at NBME.org Wed Nov 28 09:07:36 2001 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Wed, 28 Nov 2001 09:07:36 -0500 Subject: [BiO BB] government contract opps Message-ID: Deat Tom: We are a group of bioinformatics professionals working in Philly/Nj area. We recently have started a training series on bioinformatics and also interested to do consulting. Please send us details or contact info, so we can discuss furthur. Thanks, -Ravi -----Original Message----- From: tom poe [mailto:tompoe at renonevada.net] Sent: Tuesday, November 27, 2001 11:01 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] government contract opps Hi: Where would be an appropriate place to post for contract opps for government agencies? I have need of three (3) bioinformatics researchers for an upcoming government contract submission. In other words, where do you folks look, when you're looking? thanks, tom _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Wed Nov 28 10:28:03 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 28 Nov 2001 10:28:03 -0500 Subject: [BiO BB] Re: government contract opps References: <01112720004001.10807@aether> Message-ID: <3C050283.8FFBBBFA@bioinformatics.org> Anyone interested in posting job opportunities or positions sought can do so at Bioinformatics.Org jobs forum (BiO Jobs): http://bioinformatics.org/news/jobs/ As with everything else at BiO, there is no charge. Agencies are welcome to use the forum too. The poster needs to be a member, however, but membership is also free. Regarding e-mail subscriptions to the forum, the subscribers list is temporarily shared with BiO News. BiO Jobs will have a separate subscription process shortly. (I.E., don't subscribe yet.) Cheers. Jeff tom poe wrote: > > Hi: Where would be an appropriate place to post for contract opps for > government agencies? I have need of three (3) bioinformatics researchers for > an upcoming government contract submission. In other words, where do you > folks look, when you're looking? thanks, tom -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From crasmen at magic.fr Wed Nov 28 12:36:52 2001 From: crasmen at magic.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Wed, 28 Nov 2001 18:36:52 +0100 Subject: [BiO BB] Re: government contract opps In-Reply-To: <3C050283.8FFBBBFA@bioinformatics.org> References: <01112720004001.10807@aether> <3C050283.8FFBBBFA@bioinformatics.org> Message-ID: At 20:00 -0800 27/11/01, tom poe wrote: >Hi: Where would be an appropriate place to post for contract opps for >government agencies? At 10:28 -0500 28/11/01, J.W. Bizzaro wrote: >Anyone interested in posting job opportunities or positions sought can do so >at Bioinformatics.Org jobs forum (BiO Jobs): > >> http://bioinformatics.org/news/jobs/ There are plenty such sites. I know many people use: http://www.sciencejobs.com/ Corentin From roumieu at genops.com Thu Nov 29 01:37:23 2001 From: roumieu at genops.com (Jordan Roumieu) Date: Wed, 28 Nov 2001 22:37:23 -0800 Subject: [BiO BB] Sequence analysis platform for OS X - inviting beta-testers. Message-ID: Dear Researchers, My company has ported its nucleotide and protein sequence analysis platform, Ngene, to OS X and is inviting beta-testers to evaluate the product. Ngene integrates applications and databases using Java and adds value to them by applying parallel computing on a Linux cluster, automating experiment management, and simplifying workflow. On Friday Nov. 30th beta-testing information will be available on the beta-download site http://www.genops.com/download/default.htm . A Windows-based trial version is already available there. Contact me for further information. Many thanks, Jordan Roumieu E-mail: roumieu at genops.com Genops Bioinformatics Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: