In any case, does Nature Methods actually publish any papers that fall into the category (quote) "custom-designed software necessary for the method's implementation" where "a software program is the focus of the report", at least in the area of macromolecular structure determination? Come to that, are its sister journals Nature or even Nature Structural & Molecular Biology well-known for publishing such papers, and is this the reason that there is not the same requirement for them?
Recently we were looking for a journal to publish precisely such a paper and on looking at the "Aims and scope of journal" (http://www.nature.com/nmeth/authors/index.html) we saw "Biomolecular structural analysis technologies, including NMR and crystallography", but then looking through the past issues we couldn't find any papers remotely similar to ours so it was way down the list of options. There is actually no absolute requirement by Nature Methods that the software be Open Source, quote "The guiding principle is that enough information must be provided so that users can reproduce the procedure and use the method in their own research at reasonable cost." and that closed-source software "may be acceptable if the operations performed by the software are sufficiently clear.". If however "the software is only an ancillary part of the method, and the focus is on the methodological approach or an insight gained from it" then "releasing the code may not be a requirement for publication". Actually I would be rather more concerned with the statement: "a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols available to readers promptly on request". "Materials" would appear to include purified and crystallised protein, at least they aren't specifically excluded, so does this really mean I'm obliged to give the 10mg of pure protein that has taken me 6 months to isolate to anyone that asks for it, even though I'm apparently allowed to charge "reasonable" costs (presumably in this case 6 months salary + overheads + all materials used). Even so, losing all my protein in this way would be a major set-back to my research program! I concede this is an extreme example but where does one draw the line? Cheers -- Ian > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Nadir T. Mrabet > Sent: 23 March 2007 18:57 > To: [email protected] > Subject: Re: [ccp4bb] Nature policy update regarding source code > > Hi, > > I believe such requirements concern only "Nature Methods" rather than > "Nature" by and large. > Regards, > > Nadir Mrabet > > Pr. Nadir T. Mrabet > Cellular & Molecular Biochemistry > INSERM U-724 > UHP - Nancy 1, School of Medicine > Avenue de la Foret de Haye, BP 184 > 54505 Vandoeuvre-les-Nancy Cedex > France > Phone: +33 (0)3.83.68.32.73 > Fax: +33 (0)3.83.68.32.79 > E-mail: [EMAIL PROTECTED] > > > > [EMAIL PROTECTED] wrote: > > I thought that some of you might be interested that the > journal Nature > > has clarified the publication requirements regarding source code > > accessibility. It is likely that some of you deserve congrats > > for this. Cheers! > > > > http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html > > > > Although there are still some small problems, I think that this is a > > big step forward, and certainly an interesting read, if you are > > interested in FOSS and science. > > > > Regards, > > Michael L. Love Ph.D > > Department of Biophysics and Biophysical Chemistry > > School of Medicine > > Johns Hopkins University > > 725 N. Wolfe Street > > Room 608B WBSB > > Baltimore MD 21205-2185 > > > > Interoffice Mail: 608B WBSB, SoM > > > > office: 410-614-2267 > > lab: 410-614-3179 > > fax: 410-502-6910 > > cell: 443-824-3451 > > http://www.gnu-darwin.org/ > > > > > > > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
