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

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. Overview. Research papers important to your work: hundreds or more

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

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  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

  2. 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, ...

  3. 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 \href{file:./FermatProof.pdf} {Modular elliptic curves and Fermat’s Last Theorem}~\cite{Wiles95} • 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)

  4. 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

  5. Searching for research articles on the Internet • scholar.google.com • “Modular Elliptic Curves” filetype:PDF • 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

  6. 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)

  7. 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

  8. 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 Alt+TAB 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

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