Papers is the new application from the folks that brought us 4Peaks and EnzymeX and other fine Macintosh programs for molecular biologists. Papers again is Macintosh-only (both PowerPC and Intel) and the first of their programs that is not free ($39 or €29 for a single user license).
Handling PDFs before Papers
Before the release of Papers, most scientists had devised their own system of storing the scientific publications most relevant to them. This could be folders with printouts sorted by topic or author or, as practically all papers are now distributed as PDF files, electronic copies stored on a computer in some filing system or another. PDF files could also be stored in reference managers such as Endnote, programs that are needed when you write your own scientific paper. But PDF support in these programs has always been something of an afterthought. For Macintosh users – and many scientists use the Mac – Sente is a wonderful reference manager with good PDF support, e.g. Sente automatically renames imported PDFs to something meaningful, e.g. by first author and publication year.
How Papers handles PDF files
Papers has taken PDF support to a new level, and the comparison to iTunes is not too far off. It is by far the best application to import all the PDF files of the scientific papers scattered around your hard drive and than match the publication record in the PubMed database. If Papers is like iTunes, than PubMed is like Gracenote, a central database of all scientific papers, maintained by the US National Library of Medicine. The nice integration with PubMed also shows when you want to import the PDF file of a publication you found in PubMed – it just couldn’t be easier.
Once you have your papers in Papers, it is a breeze to find and print out a paper. This is what you will end up doing most of the time, and it is faster and less space-consuming than reaching for that folder with the printouts in your bookshelf. What makes Papers such a pleasure to use is not just the basic idea of handling the PDFs of scientific papers in the best possible way, but do it with the look and feel and attention to detail that we love in a good Macintosh application. One of the features I like in particular is the PubMed search interface. It makes it very easy to use the more advances search features of PubMed.
Still at version 1.0
Papers is at version 1.0.1, so expect a few version 1.0 quircks – from sometimes sluggish behaviour to little interface bugs. What I would like most to see in version 1.1 is a better way of handling the way most scientists look out for new literature. One common approach is to scan new issues of the most important journals in your area of interest for articles relevant to your work. Most journals send out emails with the table of contents (TOC) once a new issue is released. More and more journals are also offering RSS feeds of the same information. In addition to scanning journal TOCs, most people will also regularly search PubMed for particular keywords, either manually or again by email notification or RSS. Papers is trying to help you with both strategies (e.g. by listing the most recent publications of a journal and linking to the table of contents), but the execution is far less elegant than the PDF handling.
Another obvious feature for version 1.1 is library sharing (again think iTunes) so that you can easily exchange references (with or without PDF files) with your coworkers. This of course touches on an aspect which is as bitterly fought in scientific publishing as is the distribution of mp3s in the music world, namely what are you allowed to do with scientific papers as almost all of them are copyrighted material. A growing number of Open Access journals allow you to freely distribute their publications, but most scientific journals don’t, not even when you are the author of the paper.
Papers is not a replacement for Endnote or other reference managers. When it comes to writing your own scientific paper, you still need them to integrate the references into your manuscript. For now, Papers can export to Endnote and other bibliography formats, but we don’t know whether Mek & Tosj have any plans in that direction for Papers 2.0.
