Tools for handling information

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I was going to write a piece called Information Management for Biomedical Scientists, with lots of fancy tricks for overcoming and streamlining information overload. It never got further than an outline, but you should be able to find something of interest here anyway.
  • Information Management for Biomedical Scientists
    • Most of this is based around OS X, because of a few specific benefits. However, you can do most of this in Windows (and maybe in Linux too, I haven't tried). The latest versions of each piece of software are probably best.
    • Literature
      • Using Safari as a web browser
        • Uses tabs, so you can have lots of abstracts open in the same window
        • Allows page titles to be rewritten on the fly in HubMed, which means you can store each abstract in a bookmark folder for later retrieval.
        • Bookmarklets - there's one for HubMed searches, and another called AllAbstracts that allows you to move from PubMed directly to HubMed.
        • OS X fonts in HubMed, for improved readability
        • Java runs fastest in Safari, so the TouchGraph applet works more smoothly.
      • Researching a new topic with HubMed
        • Start with a few keyword searches. Select the most relevant articles and add them to the clipboard.
        • From the clipboard, select the 4 or 5 best matches and use 'Rank Relations' to show new articles that are most closely related to all of the original articles. Select the most relevant of these and add them to the clipboard.
        • Follow the links in the 'References' section for each abstract to find other relevant papers that cited or were cited by the articles already collected, and add them to the clipboard
        • Add items from the clipboard to a TouchGraph (PubMed Browser). Unfortunately you have to do this one at a time at the moment, using their ID numbers, but it's worth the effort. Select any new articles (follow the link in the 'info' window) and add them to the clipboard.
        • Finally, select the whole clipboard and use the 'Make A List' button to store it in biologging for others to find, adding a title and description as well - if you prefer not to use biologging, you can select the whole clipboard and export all the abstracts to Endnote instead.
      • Regular updates of newly published articles
        • Monthly Tables of Contents
          • Individual journal/publisher sites provide updates by email (see also ZETOC, Infotrieve)
          • Subscribe only to the few that you actually read
          • Use the filtering in Mail (or POPFile for Windows) to avoid junk mail
        • Daily updates
          • HubMed RSS feeds
            • Drag the XML button from a HubMed search into your preferred news aggregator
          • NetNewsWire (news aggregator)
            • View > Aggregated new items - shows all searches on one page
            • View > Combined view - shows all abstracts on one page
            • Preferences > Open pages in background - opens abstracts in a new browser window when selected, so you can read through them and collect the papers later.
      • Individual papers
        • Direct links to fulltext from HubMed (via NCBI LinkOut service). Also indirect links via SFX, if the direct link isn't available
        • Download as PDF
        • Save the file as AuthorYear, eg 'eaton03'. to make it easy to find and identify later.
        • Catalogue with DEVONthink (see also dtSearch for Windows)
          • Use OS X's Folder Actions to automatically import files into the DEVONthink database when they are added to a particular folder. To do this you need to use two of the standard Applescripts - 'Add Action to Folder' and 'Enable Folder Actions'. Put them in '/Library/Scripts', and put 'Action Import' (comes with DEVONthink) in '/Library/Scripts/Folder Action Scripts'. Run 'Enable Folder Actions', then run 'Add Action to Folder' and select the appropriate script and folder as directed.
          • PDFs are converted to Rich Text Format with Text Lightning when imported, allowing searching and analysis.
          • Customise the toolbar so that 'Launch' is easily available - opens the PDF in Acrobat for easier reading.
        • Acrobat
          • Use the Highlighting and Underlining Tools to mark up the text
          • For each tool, show the Properties Toolbar
            • Uncheck 'Keep Selected' and choose a colour for highlighting
          • Read through the paper, highlighting and adding comments (the comments box appears after highlighting) as needed.
          • Save the file when finished.
          • If needed, you can copy and paste reference lists directly from the PDF into HubMed's Citation Finder to follow up references (note: if copying is restricted, you can sometimes use 'Document Properties' to set the security settings to allow copying).
        • Blogging
          • After reading a paper, find the abstract on HubMed and use Blog This to open the biologging window.
          • Add your description of the paper and a useful headline, then post to biologging.
          • Your weblog will be available from the biologging front page, and anyone can subscribe to your RSS feed.
          • A Trackback will be sent to HubMed so others can read your comments on that paper.
          • Soon, you will be able to export all your (or anyone else's) references from biologging complete with the attached notes, drectly into Endnote.
          • Once you have the reference in your Endnote library, link the PDF file into the appropriate field.
          • (If you don't want to use biologging, export the citation to Endnote earlier, add your notes directly into the notes field and link the PDF).
    • Experiments
      • Filing
        • Paper copy - Each experiment stored separately
        • Digital copy - 1 folder per experiment, named YearMonthDay (eg 030726) to allow alphanumerical sorting.
      • Protocols - OmniOutliner
        • Print out the protocol before you start
        • Add notes to this sheet as you go along
        • Keep in paper file
        • Adjust protocol as needed - save an electronic copy of the protocol used in the date folder, and save the master copy for next time.
      • Results
        • eg Excel for spreadsheets, Prism for statistics and graphing, FlowJo for flow cytometry data analysis
        • Save digital copy of data in date folder
        • Results layout page (just the important pictures) - print paper copy and save digital copy as PDF in date folder
      • Notebook
        • Blosxom
          • Fully customisable weblog
          • Entries stored as text files
          • Entries sorted chronologically
          • Blosxom 2.0 with plugins - search
        • Blapp
          • Allows editing entries without changing the date. Can use the UNIX command 'touch' from the Terminal to set the date if necessary, but this is awkward enough that it acts as an incentive to write up an experiment on the same day.
          • Drag in links from browser history and bookmarks to add context
          • Set folder for saving entries - allow different categories if required.
        • Allow viewing from a remote computer (eg a supervisor) by setting a username + password or a particular IP address in the .htaccess file. (see overview)
    • Writing papers/dissertations/theses
      • Word for text
        • Use Outline view to assign levels to each heading
        • Use 'Format Style' to change appearance of the text (as with CSS)
        • Use 'Add Caption' to assign figure and table captions
        • All this makes it easy to automatically generate Table of Contents, and quick to make changes to format and style.
      • Endnote for references
        • Integrates well with Word
        • Export/import from other bibliographic software as RIS format
        • Provides Word templates for writing papers for many journals
        • Edit the ouput style to make sure it's correctly formatted for the journal
      • Prism for statistics and graphing
        • Try the demo version
      • Photoshop or Graphic Converter for image manipulation
      • OmniGraffle for flow diagrams
      • Illustrator for illustrations
    • Other software
      • iCal for outlining experiments, seminars, meetings etc
      • VoodooPad for storing random notes
      • Powerpoint or Keynote for presentations
      • iChat or Fire (Trillian or Miranda for Windows) for instant conversations with others
      • Rendezvous and Hydra to collaborate when writing documents?
    • Set up all the lab computers using OS X and Windows XP so that each user has an individual account. Then you can switch on file sharing and each user will be able to connect to their files on another computer without causing a security risk for anyone else. Doing this also means that each user can have their own settings, email, favourites, desktop etc.
    • Set up a lab webpage so other people can find out what you do.