TDI-discuss

tdi-discuss@salilab.org

36 discussions

Suggestion
by Toni Hermoso 16 Feb '05

16 Feb '05

I wanted to add the wiki some DB, proteomic and genomic resources I have been using in my own bioinformatics work and I think that could be useful for approaching a research project. For instance for Plasmodium: http://plasmodb.org Some references to typical tutorials or guides on how using BLAST and other tools could be useful for the bioinformatics work, especially for beginners who are starting with the project, as some of you have pointed... It could be nice to link journals where there could be updated information relevant for the research on these topics. For instance, for Plasmodium: http://www.malariajournal.com/ Do you have any suggestion for a hierarchy for the wiki? What do you think about something such as: - Diseases: - Malaria - Dengue - etc - Organisms: - Human - Rat - Anopheles - Plasmodium - Programs - BLAST - Modeller - etc. - Methodology etc Regards, -- * Toni Hermoso Pulido ------------------------------------------------------ web: http://drac.homelinux.org email: toni(a)salilab.org toniher(a)softcatala.org gpg: B67B43DC All that you touch You Change. All that you Change Changes you. The only lasting truth is Change O.Butler ------------------------------------------------------

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Re: let's talk about the barriers
by Peter Gorzinsky 16 Feb '05

16 Feb '05

I just read an article in the Economist about Cambia's open source project and then visited their site--www.bioforge.net From what I could see, it seems to be working well. You should check it out. --Peter __________________________________ Do you Yahoo!? Read only the mail you want - Yahoo! Mail SpamGuard. http://promotions.yahoo.com/new_mail

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volunteer
by HUBIE2001＠aol.com 16 Feb '05

16 Feb '05

Hello, My name is Adam Huber and I am a medical student at UNSW in Sydney Australia. I am interested in beginning research focused on tropical and infectious disease for underserved populations (A mission that seemingly matches TDI). I am, however, confused. If someone will tell me where to sign up and give me some research topics to begin on, I'd be greatful. hergenro(a)msu.edu Thank you kindly, Adam Huber

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Obituary: William Trager
by Dr. Alfonso J. Rodriguez 25 Jan '05

25 Jan '05

Date: 25 Jan 2005 From: Jerome Vanderberg <jerome.vanderberg(a)med.nyu.edu> Via: ProMED-mail<promed(a)promedmail.org> This is to inform all of his friends and admirers that Dr. William Trager, one of the prime leaders in malariology, died at home last Saturday night. He had had mild influenza last week but began feeling worse Saturday night, then suffered a heart attack 2 hours later. Dr. Trager was about 95. He remained active, going to his office at the Rockefeller University 3 days a week. Several colleagues reported having had scientific discussions with him over the last few months, so he was going strong until the very end -- exactly as he would have liked and as we all might have expected of him. Bill Trager was a talented, inspired, inspiring, insightful and honest scientist, and was one of the most decent human beings that I ever had the privilege of knowing. He will be missed. -- Professor Trager received the Prince Mahidol Award in 1994 (named in honor of the Thai Prince). The award statement included the following: <http://kanchanapisek.or.th/pmaf/awardees/1994.en> "Professor William Trager, a protozoologist and an authority on tropical medicine and insect physiology, is a leader in the fight against malaria, the most prevalent disease in the world today. In 1976, he and a colleague described a practical method for the continuous cultivation of _Plasmodium falciparum_, the most highly pathogenic human malaria parasite. Adopted by laboratories around the world, this method has given rise to a spectrum of physiological, biochemical, immunological, and genetic studies that were previously impossible or prohibitively difficult, opening the way for scientists working to develop an effective malaria vaccine. _P. falciparum_ cultures have also advanced work on malarial drug resistance and efforts to screen for new types of antimalarial compounds. Dr. Trager's malaria reseach began 60 years ago, when he provided the first direct evidence of the significance of nutritional factors in the host's susceptibility to malaria. Since then, he has shown that intracellular parasites lack certain biosynthetic pathways and depend on their host cells for cofactors essential to their own metabolism. His laboratory provided the 1st demonstration of the fine-structural relationship between malaria parasites and their host red cells. They also elucidated the cellular and physiological basis for the relative resistance to malaria conferred by the sickle haemoglobin gene. Recently, they achieved axenic cultivation of _P. falciparum_, obtaining extracellular development of the complete erythrocytic cycle, work that may permit new research on the nature of the parasite's dependence on its host. Methods developed for extracellular cultivation of _P. falciparum_ may also be applicable to other parasites that have resisted cultivation, including other human malaria parasites. Other contributions include early studies on the nutritional needs of the larvae of _Aedes aegypti_, the yellow fever vector; demonstration of the mechanism of acquired immunity to ticks; and development of cultivation methods for a principal trypanosomal parasite of cattle. Professor William Trager graduated with a B.S. from Rutgers University and received a Ph.D. from Harvard University. He spent his entire professional career at the Rockefeller University, where he became a Professor Emeritus in 1980 and remains active as head of the laboratory of parasitology. " ______________________________________________ Renovamos el Correo Yahoo!: ¡250 MB GRATIS! Nuevos servicios, más seguridad http://correo.yahoo.es

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Wiki Vandals
by Stephen Mark Maurer 25 Jan '05

25 Jan '05

Dear All, The Wiki was vandalized again this morning, I've asked our hosts if they can do something to stop it. Apologies for the inconvenience. steve

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XVII Latinamerican Congress of Parasitology - Argentine 2005
by Dr. Alfonso J. Rodriguez 24 Jan '05

24 Jan '05

Information of the XVII Latinamerican Congress of Parasitology IV Argentine Congress of Parasitology XXIX International Meeting of Hidatidology 23 - 26 November, 2005 Mar del Plata, Argentine. Abstracts deadline: 15 July 2005. Web Site: http://www.mdp.edu.ar/seminarios/flapxvii/ ______________________________________________ Renovamos el Correo Yahoo!: ¡250 MB GRATIS! Nuevos servicios, más seguridad http://correo.yahoo.es

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Fw: Open Source Stem Cell R&D (fwd)
by Luca Brivio 24 Jan '05

24 Jan '05

This seems to be interesting, although not so related to TDI... Begin forwarded message: Date: Sat, 22 Jan 2005 18:23:25 +0100 (CET) From: Andreas Tille <tillea(a)rki.de> To: Debian Med Project List <debian-med(a)lists.debian.org> Subject: Open Source Stem Cell R&D (fwd) Hi, I did not really found a download or a license but if there is any interest someone might do a more detailed research on the home page http://usbiodefense.com/news_012105.php which seams responsible for the message on LinuxMedNews: http://linuxmednews.com/linuxmednews/1106324091/index_html U.S. BioDefense to Launch Open Source Platform for Rapid Stem Cell Research and Development. Read on for the complete announcement. City of Industry, CA January 21, 2005 - U.S. BioDefense, Inc. (OTCBB: UBDF) announced today that it is developing an Open Source Stem Cell Research Platform to leverage the distributed power of open source development. The Open Source Stem Cell Research Platform will allow researchers at Universities, Government Agencies, and Fortune 500 companies to read, distribute, modify and contribute to stem cell and biotechnology research in an efficient and streamlined method. The platform which can be used as an Intranet or online will provide access to bioinformatic tools and serve as a robust utility for the rapid evolution of Stem Cell technology research, development, and commercialization. U.S. BioDefense CEO David Chin stated, We intend to quickly scale up revenues by focusing on selling Open Source collaborative technology research and transfer tools as well as commercializing leading edge technology. The proliferation of open source development to industries beyond software has prompted U.S. BioDefense to aggressively lead the drive in implementing the philosophy and benefits to the emerging stem cell industry. We are positioning ourselves at the nucleus of Stem Cell research and development tools in order to leverage the potential of California's $3 Billion Stem Cell Research Fund and our Department of Defense SBIR Grant response related to Embryonic Stem Cell technology for Bioengineered skin commercialization. U.S. BioDefense is aggressively pursuing its technology transfer initiative by incorporating the distributed power of open source development in individual biotechnology fields related to biodefense research beginning with its Stem Cell commercialization initiative. The Open Source Stem Cell Research Platform being developed by U.S. BioDefense is an adaptation of the monumental open source movement in software development that has also been embraced by large technology companies like IBM (NYSE: IBM), Novell and Sun Microsystems (Nasdaq: SUNW). According to Wired Magazine recently the idea of open source biotechnology has been gaining momentum with the introduction of BIOS, the Biological Innovation for Open Society (www.bios.net), a non profit with the support of The Rockefeller Foundation encompassing the creative use of living systems and their environment, and with the implementation of open source principles and development methods in the field of bioinformatics. According to BIOS web site the organization will create a mechanism BioForge by which like-minded individuals and agencies can collaborate with optimum effectiveness to solve problems and create technologies under an open-access regime. The goal of BioForge is to forge a dynamic protected commons of enabling technologies that will be available to the worldwide inventive community for use in improvement and new innovations. The VA Software SourceForge.net Open Source network provides a scalable solution for empowering development teams across the diverse worldwide Open Source community. Today, SourceForge.net is the world's largest Open Source software development web site, hosting more than 90,000 projects and over 950,000 registered users. OSTG receives more than 230 million page views and over 16 million unique visitors every single month. About U.S. BioDefense, Inc. U.S. BioDefense is a Department of Defense central contractor that researches, develops, and commercializes leading-edge biotechnology. U.S. BioDefense recently announced that it had filed its Small Business Innovation Research (SBIR) Grant proposal Number C051-117-0060 with the Department of Defense Chemical Biological Defense Agency in response to SBIR (dodsbir.net) Topic number CBD05-117 'Stem Cell Technology And Autologous Bioengineered Skin For The Treatment of Cutaneous Vesicant Injury'. U.S. BioDefense recently sponsored the Project T2 Technology Transfer Conference, the nation's leading showcase of new university technologies, being hosted at the Wilshire Grand Hotel in Los Angeles, CA. Other sponsors (http://www.projectt2.org/sponsors.htm) include Southern California Edison, Latham & Watkins, Morrison & Foerster, PricewaterhouseCoopers, Canadian Consulate General, and Genzyme (NYSE: GENZ). U.S. BioDefense, Inc. recently entered into a Commercial Evaluation License Agreement with the National Institutes of Health (NIH). The biotechnology is related to a method for universal inactivation of viruses, parasites and tumor cells. These inactivated agents can be used as vaccines against the diseases caused by such viruses, parasites and tumor cells. Hence, the immunogenic of the agent as a whole is maintained and can be safely used for vaccination without the threat of infection. U.S. BioDefense, Inc. intends to conduct laboratory experiments under this Agreement to evaluate the suitability for commercial development. Furthermore, U.S. BioDefense, Inc. has agreed to provide the facilities, personnel, and expertise to evaluate the commercial applications. NIH's bioterrorism budgets have jumped from $53 million in 2001 to $1.7 Billion in 2005. Safe Harbor Statement Forward-Looking Statements Included in this release are certain forward-looking'' statements, involving risks and uncertainties, which are covered by the safe harbor provisions of the Private Securities Litigation Reform Act of 1995, including statements regarding the Company's financial performance. Such statements are based on management's current expectations and are subject to certain factors, risks and uncertainties that may cause actual results, events and performance to differ materially from those referred to or implied by such statements. In addition, actual future results may differ materially from those anticipated, depending on a variety of factors, including continued maintenance of favorable license arrangements, success of market research identifying new product opportunities, successful introduction of new products, continued product innovation, the success of enhancements to the Company's brand image, sales and earnings growth, ability to attract and retain key personnel, and general economic conditions affecting consumer spending, including uncertainties relating to global political conditions, such as terrorism. Information with respect to important factors that should be considered is contained in the Company's Annual Report on Form 10-K as filed with the Securities and Exchange Commission. Readers are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof. The Company does not intend to update any of the forward-looking statements after the date of this release to conform these statements to actual results or to changes in its expectations, except as may be required by law. CONTACT: U.S. BioDefense, Inc. David Chin, 626-961-0562 info(a)usbiodefense.com < | Washington Monthly: The Best Care Anywhere > -- To UNSUBSCRIBE, email to debian-med-REQUEST(a)lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmaster(a)lists.debian.org -- Luca Brivio Web: http://icebrook.altervista.org Jabber: lucab83(a)jabber.org ________________________________________________________________________ "Homo sum: humani nil a me alienum puto" (P. Terentius Afer) ________________________________________________________________________

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NIH Molecular Libraries
by Stephen Mark Maurer 20 Jan '05

20 Jan '05

Dear All, Saira Mian sent this along, does it fit in somehow? +++++++++++++++++++++++ +++++++++++++++++++++++ http://www.sciencemag.org/cgi/content/full/306/5699/1138 NIH Molecular Libraries Initiative Christopher P. Austin, Linda S. Brady, Thomas R. Insel, and Francis S. Collins austinc(a)mail.nih.gov The purpose of the Molecular Libraries Initiative (MLI) component of the NIH Roadmap for Medical Research (1, 2) is to expand the availability, flexibility, and use of small-molecule chemical probes for basic research. ... In exceptional circumstances, the NIH itself might attempt the subsequent steps of drug development, particularly if a small-molecule probe shows special potential for development into a drug for an orphan indication or a disease occurring primarily in the developing world, where there is unlikely to be commercial interest. In this case, NIH Roadmap mechanisms such as the Translational Research Core Services Program and the Regional Translational Research Centers (20) could be used. -- I. Saira Mian Life Sciences Division (Mail Stop 74-197) E-mail: SMian(a)lbl.gov Lawrence Berkeley National Laboratory Telephone: (510) 486-6216 1 Cyclotron Road Facsimile: (510) 486-6949 Berkeley, California 94720-8265

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Science Plan
by Stephen Mark Maurer 19 Jan '05

19 Jan '05

Dear All: The Wiki seems to be stable, at least for now. Sorry for all the problems. Meanwhile, Dr. Saira Mian here in Berkeley has been thinking hard about the kinds of science that TDI might want to do. I've posted her outline on the Wiki Activities page: tdi-discuss(a)tropicaldisease.org Since I'm a lawyer, I'll spare you my biology opinions. However, I do think that she's absolutely right to be focusing on nuts-and-bolts science issues. If we do the science well, I'm optimistic that the rest of TDI will fall into place. So please, take a hard look at the activities page and be creative! steve steve

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The Wiki is Back
by Stephen Mark Maurer 13 Jan '05

13 Jan '05

Dear All, The Wiki was apparently attacked by spammers. Our friend at NATURE cleaned up most of the problem, but if it recurs we will do something to lock out random spammers. I notice there's already a bit of stuff this morning. In the meantime, enjoy the site. I've been waiting a long time to hear what all of you have to say! steve

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