Re: Bibliography and File Management
On Sun, Mar 15, 2009 at 7:09 AM, David Schryer wrote: > Give Zotero a try. It has adequate (but not perfect) BibTeX output which > can be cleaned up in jabref easily. Collecting, annotating, and organizing > the database is made easy with tags and associations, and it captures the > pdf directly from the host site and includes DOI, ISSN, ISBN, and loads of I tested Zotero earlier this morning and I found that it does not capture PDFs, even when Google Scholar clearly, explicitly links to the PDF for an article of a citation that is imported. Are there any tools that fix this behavior? - Bryan http://heybryan.org/ 1 512 203 0507 -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Bibliography and File Management
Give Zotero a try. It has adequate (but not perfect) BibTeX output which can be cleaned up in jabref easily. Collecting, annotating, and organizing the database is made easy with tags and associations, and it captures the pdf directly from the host site and includes DOI, ISSN, ISBN, and loads of other info. You can also associate any arbitrary file, note, link, to all records, so it is easy to include many layers of info in one database. The new collaborative features seem to work, but I have yet to test them in a serious multi-user environment yet. Even though this sounds like advertising, I am just a user who has tried loads of other tools over many years and like this one. The only slight downside is it slows down firefox on some sites, so I only use it when I am collecting references. Happy reading, David On Sun, Mar 15, 2009 at 10:42 AM, Alastair McKinstry < alastair.mckins...@sceal.ie> wrote: > > On 14 Mar 2009, at 23:28, Bryan Bishop wrote: > > On Sat, Mar 14, 2009 at 6:23 PM, Benda Xu wrote: >> >>> I have downloaded a lot of papers from the journals for reading and >>> reference. Although I tried to develop a naming scheme to organize the >>> file (mostly PDF format), I run into chaos these days: I forget which is >>> which before actually open the files one by one. >>> >> >> Yes, I run in to this problem as well. I go on reading sprees of >> hundreds of papers. Recently it was something like 200 papers and 150 >> MB re: microfluidics. BibTeX is nice, but not always a given. Google >> Scholar allows you to export citations as you find paper search >> results- perhaps it would be possible to write a userscript/javascript >> hack that would automatically download the BibTeX citation as you >> download a file? This way, you always keep track of information per >> download. This is a hack, not a real solution, of course. >> >> > Another program to include (is it in squeeze?) is calibre. I use an ebook > reader to read many papers and books; > it keeps its own metadata and book / paper sets: the pdfs are kept in a > filestystem (fine); some synchronisation of > the metadata and papers with a bibtex, etc. citation list would be good. > > Another point: DOIs. Most (?) papers these days are labelled with a unique > DOI (see dx.doi.org) . This could be used > as a pointer to the paper(s) and for labelling caches. > > - Bryan >> http://heybryan.org/ >> 1 512 203 0507 >> >> >> -- >> To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org >> with a subject of "unsubscribe". Trouble? Contact >> listmas...@lists.debian.org >> >> > Regards, > Alastair > > -- > Alastair McKinstry , http://blog.sceal.ie > > Anyone who believes exponential growth can go on forever in a finite world > is either a madman or an economist - Kenneth Boulter, Economist. > > > > > > -- > To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact > listmas...@lists.debian.org > >
Re: Bibliography and File Management
On 14 Mar 2009, at 23:28, Bryan Bishop wrote: On Sat, Mar 14, 2009 at 6:23 PM, Benda Xu wrote: I have downloaded a lot of papers from the journals for reading and reference. Although I tried to develop a naming scheme to organize the file (mostly PDF format), I run into chaos these days: I forget which is which before actually open the files one by one. Yes, I run in to this problem as well. I go on reading sprees of hundreds of papers. Recently it was something like 200 papers and 150 MB re: microfluidics. BibTeX is nice, but not always a given. Google Scholar allows you to export citations as you find paper search results- perhaps it would be possible to write a userscript/javascript hack that would automatically download the BibTeX citation as you download a file? This way, you always keep track of information per download. This is a hack, not a real solution, of course. Another program to include (is it in squeeze?) is calibre. I use an ebook reader to read many papers and books; it keeps its own metadata and book / paper sets: the pdfs are kept in a filestystem (fine); some synchronisation of the metadata and papers with a bibtex, etc. citation list would be good. Another point: DOIs. Most (?) papers these days are labelled with a unique DOI (see dx.doi.org) . This could be used as a pointer to the paper(s) and for labelling caches. - Bryan http://heybryan.org/ 1 512 203 0507 -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Regards, Alastair -- Alastair McKinstry , http://blog.sceal.ie Anyone who believes exponential growth can go on forever in a finite world is either a madman or an economist - Kenneth Boulter, Economist. -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Bibliography and File Management
David Bremner writes: > Since like emacs, you might investigate org-mode. It is good at > linking things together, and in the latest versions there is some > support for exporting bibtex. You could make a tree of topics with > links to pdf files, and tags if the hierarchy is too restricting. Great. I will try org-mode to see if it can fit my need. Cheers! -- Benda Xu Academic Talent Program, Fundamental Science of Mathematics and Physics, Tsinghua University, P.R.China http://alioth.debian.org/~heroxbd-guest -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Bibliography and File Management
Benda Xu wrote: >There will certainly be more and more papers I collect and I am >wondering a smart way to manage the references. >I do not have a full desktop environment. I would like a CUI friendly >(esp. Emacs friendly) tool for the same purpose. RefTeX coming with >AucTeX seems not to associate its entries with actual files locally. I >searched the web with no luck. Since like emacs, you might investigate org-mode. It is good at linking things together, and in the latest versions there is some support for exporting bibtex. You could make a tree of topics with links to pdf files, and tags if the hierarchy is too restricting. David -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Bibliography and File Management
On Sat, Mar 14, 2009 at 6:23 PM, Benda Xu wrote: > I have downloaded a lot of papers from the journals for reading and > reference. Although I tried to develop a naming scheme to organize the > file (mostly PDF format), I run into chaos these days: I forget which is > which before actually open the files one by one. Yes, I run in to this problem as well. I go on reading sprees of hundreds of papers. Recently it was something like 200 papers and 150 MB re: microfluidics. BibTeX is nice, but not always a given. Google Scholar allows you to export citations as you find paper search results- perhaps it would be possible to write a userscript/javascript hack that would automatically download the BibTeX citation as you download a file? This way, you always keep track of information per download. This is a hack, not a real solution, of course. - Bryan http://heybryan.org/ 1 512 203 0507 -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
