How to build your research paper database one PDF at a time

1
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?
• 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
• The described tool creates an index to your PDF
  files
• Based on free software Latex, Emacs, Adobe
  Acrobat, ...

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Basic layout for building the index to your PDF
files

• index.tex
• Each entry item you create specifies the PDF
  file, title of the article, and citation
• \item \hreffile./FermatProof.pdf Modular
  elliptic curves and Fermats Last
  Theorem\citeWiles95
• index.bib
• Each bibliography item provides the citation,
  author, title, etc.
• Use Entry-Types menu in Emacs for empty fill-in
  template
• 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

• The index tool is a simple approach to organizing
  your research docs
• Click on a title ? corresponding research article
  appears
• 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

• scholar.google.com
• Modular Elliptic Curves filetypePDF
• Only PDF documents are displayed
• www.google.com (search based on page rank)
• www.vivisimo.com (folders organized based on
  clustering)
• Use these and other search engines instead of
  relying only on one

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Research article databases (subscription required)

• www.webofscience.com
• www.ieeeexplore.com
• www.sciencedirect.com
• www.cas.org/SCIFINDER/SCHOLAR
• www.arxiv.org (no subscription required)

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Remote collaboration using VNC

• 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
• 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

• Cygwin (www.cygwin.com)
• Unix-like shell for your Windows file system
• Emacs (www.xemacs.org)
• Spell check, auto-fill mode, syntax highlighting
• Virtual desktops (e.g., search for JS Pager)
• Useful for laptops with small screens
• For Windows, use AltTAB to cycle among active
  applications
• Firefox browser (www.mozilla.org/products/firefox)
  
• Tabbed browsing, block pop-up ads, scrapbook
• http//addons.mozilla.org for more extensions