How to build your research paper database one

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 SLL 1

Overview l Research papers important to your work: hundreds or more l Source: online journals, author websites, your own material l What ever happened to the notion of a “paperless office”? l Need a tool for quick access to titles, bibliography, article itself l Such a tool is useful when — reading articles and developing ideas — writing journal articles and grant proposals l The described tool creates an index to your PDF files l Based on free software: Latex, Emacs, Adobe Acrobat, . . . SLL 2

Basic layout for building the index to your PDF files l index. tex — Each entry item you create specifies the PDF file, title of the article, and citation — item href{file: . /Fermat. Proof. pdf} {Modular elliptic curves and Fermat’s Last Theorem}~cite{Wiles 95} l index. bib — Each bibliography item provides the citation, author, title, etc. — Use Entry-Types menu in Emacs for empty fill-in template l Makefile — make index (creates index. pdf) — make backup (creates the backup file index. tar. gz) — make l (displays the usage information given above) style files (2) and journal abbreviations (acronyms. bib) SLL 3

Additional notes on managing PDF documents l The index tool is a simple approach to organizing your research docs: l Click on a title corresponding research article appears l Click on a citation bibliographic information is presented l Other approaches are possible, of course l Within a PDF document, the search command is a useful feature l Google Desktop allows you to search your own files l For Apple users: — Bib. Desk is a comparable tool, a graphical bibliography manager — Apple Spotlight lets you search within all your PDF documents SLL 4

Searching for research articles on the Internet l scholar. google. com — “Modular Elliptic Curves” filetype: PDF — Only PDF documents are displayed l www. google. com (search based on page rank) l www. vivisimo. com (folders organized based on clustering) l Use these and other search engines instead of relying only on one SLL 5

Research article databases (subscription required) l www. webofscience. com l www. ieeeexplore. com l www. sciencedirect. com l www. cas. org/SCIFINDER/SCHOLAR l www. arxiv. org (no subscription required) SLL 6

Remote collaboration using VNC l 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 l 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 SLL 7

Other software and applications l Cygwin (www. cygwin. com) — Unix-like shell for your Windows file system l Emacs (www. xemacs. org) — Spell check, auto-fill mode, syntax highlighting l Virtual desktops (e. g. , search for JS Pager) — Useful for laptops with small screens l For Windows, use Alt+TAB to cycle among active applications l Firefox browser (www. mozilla. org/products/firefox) — Tabbed browsing, block pop-up ads, scrapbook — http: //addons. mozilla. org for more extensions SLL 8