How to build your research paper database –
one PDF at a time
Steven L. Lee
Center for Applied Scientific Computing
Lawrence Livermore National Laboratory
UCRL-PRES-213010
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Overview

Research papers important to your work: hundreds or more

Source: online journals, author websites, your own material

What ever happened to the notion of a “paperless office”?
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Need a tool for quick access to titles, bibliography, article itself

Such a tool is useful when
— reading articles and developing ideas
— writing journal articles and grant proposals
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The described tool creates an index to your PDF files
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Based on free software: Latex, Emacs, Adobe Acrobat, ...
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Basic layout for building the index to your PDF files
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index.tex
— Each entry item you create specifies the PDF file, title of the article,
and citation
— \item \href{file:./FermatProof.pdf} {Modular elliptic curves and Fermat’s Last
Theorem}~\cite{Wiles95}
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index.bib
— Each bibliography item provides the citation, author, title, etc.
— Use Entry-Types menu in Emacs for empty fill-in template
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Makefile
— make index
(creates index.pdf)
— make backup (creates the backup file index.tar.gz)
— make

(displays the usage information given above)
style files (2) and journal abbreviations (acronyms.bib)
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Additional notes on managing PDF documents
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The index tool is a simple approach to organizing your research docs:
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Click on a title  corresponding research article appears
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Click on a citation  bibliographic information is presented

Other approaches are possible, of course

Within a PDF document, the search command is a useful feature

Google Desktop allows you to search your own files

For Apple users:
— BibDesk is a comparable tool, a graphical bibliography manager
— Apple Spotlight lets you search within all your PDF documents
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Searching for research articles on the Internet
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scholar.google.com
— “Modular Elliptic Curves” filetype:PDF
— Only PDF documents are displayed

www.google.com (search based on page rank)
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www.vivisimo.com (folders organized based on clustering)
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Use these and other search engines instead of relying only on one
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Research article databases (subscription required)
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www.webofscience.com
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www.ieeeexplore.com
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www.sciencedirect.com
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www.cas.org/SCIFINDER/SCHOLAR
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www.arxiv.org (no subscription required)
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Remote collaboration using VNC
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VNC – Virtual Network Computing
— www.realvnc.com
— Software makes it possible to view and fully interact with one
computer from any other computer on the Internet
— A valuable tool for remote collaboration
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Tips
— A free edition is available, and sufficient for most purposes
— Download is available for most operating systems
— See installation instructions and FAQ for details
— Can run in interactive or view-only mode
— To determine your IP address: www.whatismyip.com
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Other software and applications
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Cygwin (www.cygwin.com)
— Unix-like shell for your Windows file system
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Emacs (www.xemacs.org)
— Spell check, auto-fill mode, syntax highlighting
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Virtual desktops (e.g., search for JS Pager)
— Useful for laptops with small screens
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For Windows, use Alt+TAB to cycle among active applications
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Firefox browser (www.mozilla.org/products/firefox)
— Tabbed browsing, block pop-up ads, scrapbook
— http://addons.mozilla.org for more extensions
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