Hi all, This email comes about because of the recent thread about bibliography management. In particular, I've always had my eye out for what sort of software should (or should not) exist for scientific papers. Some immediate examples:
AutoScholar http://heybryan.org/projects/autoscholar/ AutoScholar is a perl script that takes a paper title and queries Google Scholar and fetches a PDF link if available- either on the first page of search results, or in the "Get This Article" link. This truly belongs as a module to the 'surfraw' project more than anything. Future bugfixes should honestly include automatically following through to the publisher's website via WWW::Mechanize and look for PDF links. PDF links are of three types usually: (1) direct links, (2) links to a page that refreshes to the PDF, or (3) a popup with some javascript black magic (like in the case of ScienceDirect) (which I don't know how to fix with perl's WWW::Mechanize, any hints?). "Call for Paper" (CFPs) file format standards- suggestions for a microformat http://heybryan.org/cfp.html """" http://wikicfp.org/ - a wiki for posting CFPs. I've posted a few. Many of the CFPs that flood my inbox are forwarded (by me) over to the wikicfp gmail e-mail address, but I know that the poor guy who runs it isn't keeping up with the CFP emails that I send his way. Also, I know that there's no automatic way of reading CFPs since they hardly have a standard format. Yes, there is standardized information that is contained within each, but not always in the same format. Anyway, CFPs should be released in a standardized format so that there is metadata, descriptions, authors/participants/keynote speakers, locations and addresses, deadlines, email addresses, URLs, BibTeX for previous proceeding publications, and so on. The wikicfp wiki has an interface for inserting information, but unfortunately it doesn't always capture all of the information of a CFP since not all CFPs follow the same three-tiered submission deadline format. What are the advantages of sending around CFP files? You could process more of them, and more quickly. You would only have to download an RSS feed or zip file of CFPs and search for terms that you are interested in. You could use the calendar/date-time information to import into your own personal calendar/scheduling system. And it might also be a good way to keep track of your work on different abstracts, posters, papers, etc., with respect to deadlines, topics, etc. Perhaps even through the submission-review-editing-(hopeful)-acceptance process? """" Recently I mentioned the idea of a GreaseMonkey userscript to complement paper-reading over Google Scholar, here on this mailing list: http://lists.debian.org/debian-science/2009/03/msg00046.html Google has an option in the user preferences page on Google Scholar ( http://scholar.google.com/ ) to show "Export citation" links next to each paper that it turns up as a result to a user's queries, including a BibTeX format. If you're downloading all of these papers, perhaps a userscript that will detect a click and simultaneously download both the PDF as well as the citation be appropriate? Or even better, perhaps exporting just the citation with the link into a queue for later processing? (This goes hand-in-hand with "list of things to improve Google with"- like "search session management" (to see recent queries, and recent results, instead of going in circles with Google Trends and Google Search History) which I'll probably never get around to implementing.) Btw, speaking of GreaseMonkey, here's a script that will fix ScienceDirect's naughty popup behavior for showing PDFs: http://userscripts.org/tags/sciencedirect http://userscripts.org/scripts/show/41663 There are some browser plugins for Firefox, such as Zotero, which does in-browser bibliography management. http://www.zotero.org/ But it's not entirely clear how often Zotero is able to capture both bibliographic information as well as the actual PDF. Anybody know? I'd like to be able to just impose a standard on all of you: a tar file with a PDF and a dot bib (BibTeX) file. But alas, this doesn't seem like it will happen. ;-) I did however have an opportunity once to impose code on PLoS ONE, but I didn't take advantage of the situation- silly me! Another software package I once put a few hours into was something I foolishly called "Autozen 2008". It was a perl script for cyclical PDF viewing- in other words, pages would be flashed up for a few seconds at a time on one of my many idle monitors. Instead of having a television blazing around in the background, when I get distracted at least I'm being distracted by something educational and interesting. "Huh. I never knew that the wetting properties of acrylic liquids was inversely proportional to their capillary crawl distance." (or something) It would also have been interesting to set up a public repository for a few clients to connect to for a "reading circle" of sorts, where we all throw in some really interesting papers, since friends and I are always talking about papers, and it's annoying copying and pasting links when we know in general the content is of high quality. For instance, sites like physorg and KurzweilAi commonly contain press releases related to some paper published in some journal, then I have to hunt through the news release to find any hints as to a citation, whereas I'm sure I know somebody who has already found the paper- which is usually more informative than the news article. So to clear up the rambling I've written above, here's some issues: (1) downloading PDFs and getting the bibliographical information easily (2) keeping track of what I have and have not read (3) keeping track of literature searching and paper-reading (4) scheduling "papers to be written deadlines" re: CFPs, managing large volumes of CFPs (5) somehow integrating the "bibtools" package into all of this (6) and also somehow integrating emacs' "org-mode" I feel that the present lack of system is somewhat broken, and I'd like to help build a toolchain, but I'd also like to see if any of these problems strike a chord with any other d-s people. Thoughts? - Bryan http://heybryan.org/ 1 512 203 0507 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
