TDI-discuss

tdi-discuss@salilab.org

36 discussions

RE: [TDI-discuss] TDI Progress Report
by Marc A. Marti-Renom 05 Aug '05

05 Aug '05

Dear all, I would like to add my 2 cents on the last submission in the mailing- list by Dr. Stephen Maurer on the meeting we held at Duke. I really recommend the lecture of his text since it nicely summarizes what we talked on the meeting celebrated last May. As you can read in the manuscript, the TDI initiative will start getting some concrete form when Dr. Kepler and his colleagues at Duke university finish the first alpha version of the target analysis system. We really hope that will give to all of us a tool to start contributing to this initiative. In my opinion, the main idea behind the new server is to allow people to annotate genes from pathogens (starting with Malaria) with the goal of generating a list of possible drug target candidates. Hopefully the server will be running before the TropMed meeting so we can get some exposure by then. I would also like to comment on the IP (Intellectual Property) discussion at the meeting. As a researcher in biology, I know that our IP are our "ideas" about what could make a difference in our research fields. To ask people to actually contribute to TDI in some form (including some "ideas") could be difficult. Therefore, there may be the need to find solutions to that particular problem. One of the solutions would be to team up with a publisher to create or use an existing journal where to publish research done with the help of the TDI effort. That would help to give credit to the people that deserves it. Additionally, the TDI server should keep record of all entries so that it is clear who and when input information into the system. This is, in my opinion, one of the topics that needs to be clarified if we want to have a successful TDI initiative. Finally, I would like to encourage all of us in the mailing list to continue discussing the points outlined in Stephen's document. We could certainly used the mailing list to add to what few of us could discuss in the last meeting at Duke. All the best, Marc ------- Marc A. Marti-Renom, Adj. Assistant Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research Mission Bay QB3. University of California, San Francisco San Francisco, CA 94143-2552 (94158 for courier delivery) Tel 1 (415) 514-4232; Fax 1 (415) 514-4231 Email marcius(a)salilab.org; Web http://salilab.org/~marcius ...

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TDI Progress Report
by Stephen M. Maurer 22 Jul '05

22 Jul '05

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Re: Leprosy in Nepal
by Marc A. Marti-Renom 01 Jul '05

01 Jul '05

Dear Dr. Macdonald, Thanks for expressing interest in the TDI initiative. Certainly Leprosy fits on the type of diseases that would best benefit from an Open Source Biology initiative like TDI. TDI is now in its initial steps and we hope that will evolve soon into something that contains more than just a web site. As we speak, some contributors are actually re-bumping the web site to add some more functionality to it so that scientists can actually start using some bioinformatics resources to do research. The intend of TDI is to compile individual contributions towards developing drugs for neglected diseases (and of course Leprosy could be one of those). Thus, TDI is a framework that allows researchers over the world (as yourself) to share ideas and results towards the goal I mention before. I really encourage you to join the TDI mailing list (http:// salilab.org/mailman/listinfo/tdi-discuss) so that you are up-to-date on the status of the initiative and maybe, in a near future, start a front on Leprosy within TDI. Sincerely, Marc ------- Marc A. Marti-Renom, Adj. Assistant Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research Mission Bay QB3. University of California, San Francisco San Francisco, CA 94143-2552 (94158 for courier delivery) Tel 1 (415) 514-4232; Fax 1 (415) 514-4231 Email marcius(a)salilab.org; Web http://salilab.org/~marcius ... On Jun 27, 2005, at 11:04 PM, Andrej Sali wrote: > > > Begin forwarded message: > > >> From: "Murdo Macdonald" <MurdoM(a)TLMNepal.org> >> Date: June 27, 2005 10:49:39 PM PDT >> To: <tdi(a)tropicaldisease.org> >> Subject: Leprosy in Nepal >> >> >> Dear Sir: >> Greetings from Kathmandu, Nepal >> I am writing to you as head of the Mycobacterial Research Lab, a >> small but active research lab which is part of Anandaban Leprosy >> Hospital >> I was very interested to come across your organisation, and >> wondered whether you have any interest in leprosy? I had a look at >> your website, but wasn't able to see any relevant information >> Thank you for your kind attention to this matter; I will look >> forward to hearing from you in due course >> >> Yours sincerely >> >> Dr. Murdo Macdonald, >> Head, Mycobacterial Research Laboratory, >> Ananadaban Leprosy Hospital, >> PO Box 151 >> Kathmandu >> Nepal >> Tel: 009771- 4290545 >> Fax: 009771- 4290538 >> E-mail: MurdoM(a)TLMNepal.org >> >> > > -- > Andrej Sali, Ph.D. > Professor and Vice Chair, Department of Biopharmaceutical Sciences > Department of Pharmaceutical Chemistry > California Institute for Quantitative Biomedical Research > University of California at San Francisco > QB3, Box 2552 > 1700 4th Street, Room 503B > San Francisco, CA 94143-2552 (CA 94158 for courier delivery), USA > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4258 > Email sali(a)salilab.org; Web http://salilab.org >

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RE: TDI-discuss Digest, Vol 6, Issue 2
by Marie Connett 09 May '05

09 May '05

You'd be very welcome to start a project with a source code control area on www.bioforge.net, which has the resources to support exactly this sort of collaborative development. BioForge is one part of CAMBIA's comprehensive approach (the BIOS Initiative) to enabling inventive and committed people within the developing world to overcome barriers to innovation. It sounds as though it's the part of CAMBIA's work that will support exactly what you suggest. We set up Bioforge to use the communications and data transfer opportunities to build useful information connections throughout the global community of problem solvers for a variety of challenges in the life sciences. We have added technology and contractual tools for analysing issues with materials and patented technology in the life sciences, though you will readily see that for pure IT it uses the same IT tools as are used by Collabnet for supporting open source software development, e.g. at java.net. The value is in having a good platform to which anyone, whether in for-profit or non-profit enterprises and whether in developed or developing countries, can bring ideas and efforts that can be pooled and probed from any time zone by members of the community, who by registering agree to share their improvements. Kind regards, Marie Connett Porceddu CAMBIA -----Original Message----- Date: Mon, 9 May 2005 11:42:03 +0100 From: "Jacob Lester" <jacob.lester(a)fdisolutions.com> Subject: [TDI-discuss] Building a knowledge base.... To: <tdi-discuss(a)tropicaldisease.org> Message-ID: <012301c55483$bdba9da0$ac34a8c0(a)fdisolutions.com> Content-Type: text/plain; charset="iso-8859-1" ....One thing that has come to mind whilst reading is the need for some sort of IT infrastructure for the TDi project, in particular a database and perhaps a source code control area (perhaps using sourceforge.net). Any thoughts on this? I was thinking of moving onto the following book (http://www.amazon.co.uk/exec/obidos/ASIN/1859960545/ref=pd_sim_b_dp_1/202-7 688707-7559031) Does anyone have any suggestions on something better? Regards, Jake ------------------------------ _______________________________________________ TDI-discuss mailing list TDI-discuss(a)tropicaldisease.org http://salilab.org/mailman/listinfo/tdi-discuss End of TDI-discuss Digest, Vol 6, Issue 2 *****************************************

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Chagas and acai
by jonwis 05 May '05

05 May '05

Can you please advise what steps, if any, can be taken to ensure that acai pulp is free of any contamination from chagas disease, or the bug faeces that cause it. Is pasteurization (heating to 85C for 90 seconds) and/or freezing likely to make any difference. Sincerely Jon Wisniewski

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What are we doing?
by Luca Brivio 14 Mar '05

14 Mar '05

I think TDI is a unique and very interesting project. I would like so much to make something for it... So, where are we going? What's happening? What can we do? I still trust in open source drug discovery. :-)) -- Luca Brivio Web: http://icebrook.altervista.org Jabber: lucab83(a)jabber.org ________________________________________________________________________ Diciamo no ai brevetti software in Europa! PerchÃ©? http://www.nosoftwarepatents.com/it/m/intro/index.html No software patents in EU! Why? http;//www.nosoftwarepatents.com/ ________________________________________________________________________

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(no subject)
by Will Rosellini 13 Mar '05

13 Mar '05

Luca, We seem to be the only people posting on both the Cambia and TDI sites. I tried to get involved with a project at BIOS but haven't heard back. I'm finishing up my paper on the bioinformatics database debate, basically my conclusion is that the EU database directive hasn't worked. The US doesn't need any additional statutory protection for databases. However, I make a distinction between genomics databases and proteomics. Genomics and the human genome being more of compilation activity, whereas proteomics is more refining information. The distinctions are important in terms of US copyright law. Btw Stephen Maurer (one of the founders of this initiative) has been very helpful. Does anyone know whether a molecular simulation, let's say a NAMD simulation of a protein is patentable? Is it copyrightable since it is code based? What about VMD visualizations of proteins? If I make a model of an amino acid, can I patent it as a program? Copyright it as a piece of art.... -Will <http://xpostmail.com/696284a28ef234987da88416302c6926worker.jpg>

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Some considerations
by Daniel Amelang 08 Mar '05

08 Mar '05

I'm a programmer, not a bioinformatician, but I stumbled across your site and thought I'd say something to keep the list active :) GNU started with RMS. He gave us programming/administration tools to play with. Linux started with Linus. He released an operating system for us to play with. You need someone great in the field to release something for everyone to 'play with'. Then people start sending patches... I know this is chicken-egg, but someone needs to point this out, since I haven't seen this brought up in the papers or the website. And you might consider merging into the bios.net effort mentioned already. Together, you just might reach the critical mass for things to take off. Consider this like when people jumped off the HURD project to come together and make linux work. Dan

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(no subject)
by Will Rosellini 28 Feb '05

28 Feb '05

So does anyone here have experience in virtual software development, open source development etc...seems like the TDI needs a plethora of bioinformatics people who can come up with a technical framework to allow contributions from people across the globe. The Open Source Biology project, Cambia's is trying but they are running into the same troubles. Does anyone know of projects, other than software development that have occurred entirely virtually? -Will <http://xpostmail.com/461a08f63e6a11f5e0d98f2d20529fc2worker.jpg>

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1st Panamerican Congress on Zoonoses - 2006
by Dr. Alfonso J. Rodriguez 22 Feb '05

22 Feb '05

1st Panamerican Congress on Zoonoses La Plata, BA, Argentina Teatro Argentino 10-12 May 2006 We very cordially invite you to attend the 1st PanAmerican Congress on Zoonoses, 5th Argentine Congress on Zoonoses, and 2nd Zoonoses Congress of the Province of Buenos Aires. The Argentine Congress takes place every other year. For 2006, the Argentine Congress and the 1st PanAmerican Congress will be combined to allow for the participation of a larger number of professionals from the region dedicated to research, prevention, and control of these diseases. The Scientific Committee invites you and colleagues to submit abstracts. The deadline for their submission is 15 Nov 2005, with complete presentations submitted by 15 Mar 2006. For more information, contact: Dr Oscar P Larghi Fray Lamas 248 1706 Haedo, BA, ARGENTINA tel: 54 11 4460 2089 fax: 54 11 4443 2971 <oplarghi(a)speedy.com.ar> <http://www.zoonosis2006.com> ______________________________________________ Renovamos el Correo Yahoo!: ¡250 MB GRATIS! Nuevos servicios, más seguridad http://correo.yahoo.es

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