History of Science Online - Course Info - Time tips - Semester Schedule - Weekly Assignments - Timeline - Projects - Course Info: HSCI 3013 - section 995 - Fall 2007

Affordable Mac apps for various academic tasks

| Mac Helps | Intro to Mac OS X | Basic setup apps from Apple and others | My paperless academic workflow |

Are you accustomed to using one application for everything? A single "kitchen sink" application that tries to do everything usually ends up doing nothing well, while locking you in and preventing future migration to new and better tools. On a Mac, things are different. The best applications tend to be small and agile, optimized to do a small number of taks extremely well. These apps work well with others, and pass information back and forth so that you can put together your own favorite, customized suite of applications that work best for your writing and research needs. Mac users work in many different ways; the abundance of high-quality Mac software may surprise you. Also, don't let their relative affordability fool you: these are superb apps. Rather than buying Microsoft Office, try Neo-Office and invest in some of the following instead. Soon you'll be wondering how you ever got anything done without them.

Word processing:

• Need to open or save Microsoft Word documents? You may be surprised, but even the lowly TextEdit (free with OS X, in your Applications folder) can open and save Word files in .doc format. TextEdit also supports Unicode, tables, and Mac OS X Services. So can the two word processors listed next.
• Mellel ($39) is the best option on any platform for writing in mulitple languages with full unicode support. Check out features like these:
  • multilingual support on OS X (e.g., Russian, Greek, Hebrew, Syriac, Arabic, Persian, etc.);
  • the ability to set a secondary language font in a specific size, as part of a paragraph style so that one may switch between similarly-sized language fonts with one click;
  • set up multiple footnote streams (e.g., footnotes, endnotes, translator notes, comments to self to hide before printing, etc.);
  • XML-based file format; or
  • support of clickable citation objects integrated with Bookends bibliographic software (described below).
  • Mellel does not crash, will not tell you what to do, lets you work in an uncluttered interface, and has superb support for outlining, styles, and page layout.
  • Mellel is rapidly evolving, with regular updates free for two years from the date of purchase.
    From the Mellel website, you can download a demo and a tutorial document. Opening the tutorial, which itself is a Mellel document, is the best way to become acquainted with Mellel. I use Mellel for all my academic writing. Don't be deceived by the price: Mellel is a full-featured word processor; you'll never miss Word. But when you have to work with someone who does, Mellel can open and save documents in the Word format.
• Pages, included with Keynote and Numbers in Apple's spectacular iWork suite ($79 academic), is the most versatile all-purpose word processor for Mac OS X and integrates seamlessly with iLife (e.g., to use your photos from iPhoto). I use Pages for any documents that incorporate images in a complex layout. Pages will open and save documents in the Word format. In fact, it works better for me in opening Windows Word documents than my own copy of Word; it will even open the latest Windows Office 07 "open XML" documents that the current Mac version of Office cannot. The latest version of Pages supports Word's Track Changes and Annotations functions when you have to collaborate with those still caught on the dark side. Many Mac using students think they need Office, but really don't. And look what else is included for that $79: Numbers has intelligent tables and many easy to use features that give you a jump-start over Excel. Keynote handles images and typefaces with a clarity that leaves PowerPoint in the dust. Try out Apple's free 30-day iWork '08 trial and see for yourself. Get iWork instead of Microsoft Office and you'll have money left over for Bookends and one or two of the notetaking programs below.
• There are also two excellent, free, open source alternatives to Word and Microsoft Office: NeoOffice and OpenOffice. Try NeoOffice first: it's based on OpenOffice, but has a more consistent Mac interface and is easier to install. Here's a NeoOffice review. Only very few Mac users would need to purchase Microsoft Office.
• A nice OS X version of Microsoft Office is available, if you need it for other classes. However, Microsoft Word is not required for this course. Because of the risk of passing on Windows viruses through Microsoft Word documents, if you send me an email with a Microsoft Word document attached, I will delete it without reading it.
• Other options are a little more geeky:
  • LaTeX (free and open source) and TextMate ($50 academic) are powerful word processors routinely used in science, engineering and technical fields.
  • BBEdit ($49) is a powerful html and text editor routinely used by programmers and web designers. Try the fully functional demo for free. TextWrangler is a free lite version, but still powerful.

Text tips:

• Dictionary, Thesaurus: TextEdit, Pages, Safari and other OS X native apps support Mac OS X's built-in Oxford American Dictionary and Thesaurus. In any OS X native application, just select a word by double-clicking it, then right-click or control-click on the word to look it up. Or, try this:
  • Place the cursor over any word, then hold down the Control and Command keys and press D (for Dictionary). The definition for your word from the Oxford Dictionary will appear as a pop-down window.
  • As long as you keep holding down the Control and Command keys, you can move the cursor over other words to see their definitions.
  • The pop-down window definitions include a "More" link; click it to open the Oxford Dictionary and Thesaurus in its own window.
• Spell-check: From the Edit menu, there is a submenu for Spelling. In the Spelling submenu, turn on "Check Spelling as you type." When you want to do a spellcheck of the document or any selected text, choose "Spelling..." from the same submenu. This Spelling submenu is a standard OS feature based on a system-level spell-checker; no need to download or install anything. It should work the same in all native applications, whether Bean or Pages or Safari or Keynote or whatever.
  • To quickly check the spelling of a single word, just double-click to select the word, then control-click (or right-click) the word. (You can also perform a Google search this way.)
• Word Service, a free download from Devon Technologies, works with any native application in OS X. Choose Statistics from the Services menu and a pane will appear displaying a count of characters, spaces, words and lines, even for read-only text such as web pages and received emails. Word Service can do many other tricks, too, such as: insert the current date; sort lines in a list; convert between all caps, first caps, and lowercase; convert straight to curly quotes or vice versa; etc.

Bibliographic management:

• Bookends is a great application for managing references and formatting in-text or footnote citations and bibliographies ($79 if you purchase Mellel; otherwise $99). You can download a demo from the Sonny Software website. It supports all major citation formats, as well as searching of online resources from Amazon to PubMed. Its clickable "citation objects" integrate seamlessly with Mellel -- yet another reason why I use Mellel for all my academic writing. Links to references may be pasted into other apps like DevonThink and OmniOutliner (see below), and these links may be converted to citations once they are imported into Mellel. Pdfs, jpgs, and other files may be attached to any bibliographic reference and opened from within Bookends (you can use Bookends as a catalog for pdfs as well as print sources; see suggestions for annotating pdfs below). In addition, the fast and personal support offered by SonnySoftware is legendary.
• Sente ($90) is the newest kid on the Mac OS X block, better looking than Bookends and designed for searching online resources. It is definitely worth a close look if you work in the sciences, but it can't handle the complex citation formats often needed in the humanities.
• BibDesk (free) is an extremely powerful bibliographic manager that integrates with BibTeX, LaTeX (all free and open source) and TextMate. TextMate has citation auto-completion via BibDesk. One of my colleagues says "BibDesk is far and away my favorite Mac application." If you work in science, mathematics, engineering or other technical fields, be sure to check these out!
• EndNote is the grand-daddy of citation managers, slow and ponderous and expensive like Office but available if you want it.

Notetaking and semi-structured writing: Past users of Microsoft Office may not realize how many excellent tools exist on the Mac for writing and researching in the early stages, before one is ready for a word processor.

• If your needs are simple, try Circus Ponies Notebook ($30). Notebook is an excellent notetaking application that combines general notetaking, outlining, and project organization. Video demonstrations are available on the Circus Ponies website. I have used NoteBook for a variety of kinds of notes, particularly ones involving multimedia, ones that are structured enough to belong in an outliner, and ones that I capture using Mac OS X services.
• If you want something more powerful and versatile than Notebook, try DEVONthink ($30), DEVONthink Pro ($60), or DEVONthink Pro Office ($113; all prices academic; see the feature comparison chart). One of the most popular academic productivity applications on the Mac, DevonThink Pro accepts most file types including video and audio, web pages, pdfs, etc.; even rss feeds. It is a digital commonplace repository for multiple file formats. If you want to juxtapose your own rich-text notes with live web pages, pdfs, images and multimedia, then DevonThink is the answer. DevonThink also offers artificial intelligence assisted classifying and searching of notes (watch the demo videos and video tutorials to see how powerful and easy-to-use the AI searching and classifying features can be). Selected text in DT can be linked to specific notes, and wiki-linking can be automated. Exporting is rich and versatile. DT has great support for AppleScripts, Automator, OS X Services, and other Mac OS X technologies. The Pro Office version supports high-quality IRIS-based OCR conversion of pdfs. In one trial, I imported a pdf I obtained through inter-library loan which contained poorly photocopied pages with different fonts, and a mixture of single pages and double-page spreads. The OCR conversion was surprisingly accurate, automatically rotating pages as needed, and in a comparison it was much faster than the OCR in Acrobat Professional. The chief limitation of DT is that it does not yet allow more than one database to be open at a time, although the developers are working on it. I now use DevonThink Pro Office as my chief research tool, for note-taking of print and pdf sources and for online searching. Here are reviews by Douglas Johnston (with an addendum) and Steven Berlin. For comparison, alternatives to DevonThink that are worth checking out include:
  • Yojimbo, with an iTunes like interface, is great for keeping track of information from any source that is not structured ($29 academic). Think of Yojimbo as a DevonThink Lite. Lacks most of DevonThink's advanced features (such as AI, or even hierarchical groups).
  • VooDooPad ($30).
  • SOHO Notes ($40).
• OmniOutliner is the premier outlining application for OS X ($39.95); included free with MacBook Pros. If you like to work from a clear outline, some projects can be written almost entirely in OmniOutliner! It exports to Keynote as well as to word processors.
• Scrivener ($35) is a drafting environment designed for notetaking and for early stages of writing. With it one can organize digital notecards on a digital corkboard. Scrivener's interface can be as simple as you like, yet there is surprising depth in its advanced features when you need them. Scrivener provides convenient tools to manage various aspects of a writing project before one exports a later draft to a word processor for final finishing. For example, you can move chunks of text around like notecards, add text formatting like italics or lists, and export as RTF files to import into Mellel or Pages for final processing. You can mark text as footnotes or comment annotations that will transfer intact to your word processor. Scrivener is an elegant writing environment for focused note-taking, outlining and drafting. I migrate notes from DevonThink into Scrivener to give them preliminary shape and coherence, and then export a well-formed draft into Mellel or Pages for final presentation and layout. DevonThink is a database to store notes and bits of information; Scrivener is a comfortable place to write and bring coherence and order to a good draft. One for capacious storage; one an elegant place to focus on writing. That is, Scrivener can help impart clarity to research in the early writing stage instead of taking notes in the everything-plus-the-kitchen-sink mode. Note: Others might prefer using OmniOutliner in this intermediary role, but Scrivener has great outlining features also if that is how you prefer to work.
  • To get to know Scrivener, watch the video tour, then download a demo, and then open and explore this sample project.
• Journler ($25) is an innovative app designed for daily entries, journaling and notetaking, and features iLife integration, video recording, and iPod exporting.
• NovaMind ($119) is a mind-mapping app that creates beautiful, colorful mind maps, which may be converted in one click to an outline document readable by any word processor. Use it for group brainstorming sessions as well. Any branch or node in the mind map may be linked to any url or file on the host computer, such as a Keynote presentation or QuickTime movie, and launched by double-clicking.
• Tinderbox ($192) is the most powerful hypertext notetaking environment on any platform.
  • Pros: It is a deep, versatile, unique approach to notetaking that offers advanced outlining, mind-mapping, whiteboarding, web publishing and much more. Screencasts and video tours are available. NotesAboutNotes.com is a blog about using Tinderbox and about notetaking in general. Tinderbox includes Yojimbo to use as a sort of quick-file temporary Inbox. In Tinderbox, any note may have any number of attributes that are user defined. You can set up prototype notes with pre-defined attributes to use as templates for any kind of note. For example, the note in this jpg screenshot is based on my "Notecard" prototype, which has pre-defined attributes for disciplines, keywords, period, source, url, etc. Powerful "agents" can perform searches and other kinds of manipulations of notes based on their attributes. Here's a review of Tinderbox that emphasizes its superb outlining capabilities. The author of Tinderbox, Mark Bernstein, has a great book about using Tinderbox entitled The Tinderbox Way. If you want the most serious and versatile notetaking tool available, download the Tinderbox demo version and give it a spin!
  • Cons: There is a learning curve to master its advanced features, such as note attributes and agents. Tinderbox lacks an OS X look and feel, and its interface sometimes behaves in not very Mac-like ways. Tinderbox does not support advanced Mac OS X features, including Applescript and Services. Exporting to a word processor is difficult, although it exports to html and is sometimes used as a blogging tool. It is designed for plain text, and does not support Unicode, nor multimedia.
• My recommendation: Download the free demos of as many of the above apps as possible. Spend a weekend seeing how they might work for you. No matter what your writing style, and no matter what variety of writing projects you have, taking a little time up front finding the right tools for digital writing and research will transform your academic life!

Digital annotations -- create a paperless workflow by marking up digital documents instead of printing them:

• Tools for annotating long pdf documents:
  • Adobe Acrobat Professional (bundled with the Adobe Creative Suite) contains unsurpassed annotation, drawing, and stamp tools for marking up pdfs, but it is an expensive and ponderous application.
  • Don't have Acrobat Professional? No worries: The free Preview application that comes with Mac OS X not only opens, indexes, and scrolls through pdf documents much faster than Adobe Acrobat, but Preview also contains useful tools for adding text and drawing ovals to any pdf. In Leopard (Mac OS X 10.5), Preview's annotation tools are much improved: you can highlight or underline text, create Pages-like notes at any point on a page, and draw rectangles and ovals around any text (later, double-click to edit, customize, or delete these shapes). You may also add links to websites and other pdf pages. Annotations can be read and edited by other users and even in Adobe Acrobat. Preview is fast and provides most of the features one needs (except for automatic exporting of highlighted text or annotated comments). In Leopard, Preview also supports dragging pages from one pdf to another, combining and splitting pdfs, and rearranging and deleting pages.
  • PdfPen ($50) is another option, with annotation and commenting tools. Like Preview, it's much faster than Acrobat and has a cleaner interface. Like Preview, it also supports drag and drop re-ordering of pages and merging pdfs, but also more. For example, it goes beyond Preview in offering standard proofreading and editing marks).
  • Skim (free) is an unbeatable bargain: It has better annotation tools than PDFpen, and gives Acrobat Professional some serious competition without being bloated. It is quick and responsive, and Mac-like. Just scan the topics in this Help page to get a sense of the depth of its features, including highlighting and commenting on text, exporting comments and notes to a separate file, and taking snapshots of diagrams or sections of a pdf. Skim also supports features that Acrobat doesn't have, such as Preview-style searching, a recently-read page indicator, a magnify tool, a nifty "snapshot" tool to keep a graph or table in view while reading further in the document, and a movable "reading bar" to keep your eye on a single line across a wide document. The chief disadvantage of Skim is that the markups are not saved in the pdf file, and so cannot be shared with others who do not use Skim unless one extra step is taken: print the pdf into to a pdf again, and the new pdf will display uneditable embedded comments. My recommendation: if you need easy exporting of annotations, use Skim instead of Preview. Here's an excellent overview of Skim by MacWorld.
  • Note on text-searchable pdfs: Before one can select text in a pdf to highlight it or copy it to the Clipboard, the pdf must contain a text layer. If a pdf does not, but is image-only, generate a text layer through OCR (optical character recognition) software. Two choices are Acrobat Professional and DevonThink Pro Office (above).
  • Tip: If an article needs scanning or a pdf needs OCR conversion, I import it into DevonThink Pro Office, which automatically does the OCR conversion to text. Then I drag it out of DevonThink in order to organize pdfs by attaching them to bibliographic records in Bookends. I read and annotate them by finding them in Bookends, which will then open them in Preview or Skim. To take notes, I create a link to the Bookends record in DevonThink or Scrivener, by dragging the Bookends reference into a DevonThink or Scrivener note. One DevonThink folder can hold all the notes I take from a single source until I'm ready to use them in Scrivener. DevonThink can also index pdfs without needing to import them. For pdfs that are not of the sort that I might cite them, I just keep them in DevonThink rather than storing them in Bookends.
• PDF managers: If you digitally annotate a lot of documents, you may wish for an organizer to manage them like iPhoto. If so, try out these:
  • Yep ($34) is billed as "iTunes for pdfs." Here's a review of Yep from MusingsFromMars.
  • Papers ($39). Papers is undergoing rapid development, and promises to include highlighting and annotation features in a future version. Both Yep and Papers are excellent tools for organizing pdfs or scanned documents, including ones you have marked up with digital annotations in the apps mentioned above.
  • Another powerful option is DEVONthink ($39.95) or DevonThink Pro Office ($113). The latter manages pdfs alongside files of many other formats, with additional features including note-taking, IRIS-quality OCR text generation and AI-assisted searching.
  • A bibliographic manager like Bookends can also attach pdfs to citation records, with links to the record that may be dragged into other apps like DevonThink, Scrivener, and OmniOutliner. I use both DevonThink Pro Office and Bookends to manage my pdfs, as explained above.
  • The economical option is iTunes (free), which manages pdfs as well as music and movies; you can even make playlists of pdfs!
       
• Tools for annotating screenshots. The MusingsFromMars blog has a review of screenshot markup utilities. Here are the two top choices:
  • ScribbleScreen (free) supports typing text and drawing with custom options, copy and paste, adjustable transparency, and screenshots.
  • FlySketch ($24.95). According to MusingsFromMars: "With FlySketch, I can quickly position the software over a digital document of any kind, take a snapshot, and begin writing or drawing my annotation. When I’m done, I can save to PDF or other image format, or I can use the built-in Applescript workflow feature to simply email the item to someone."
  Preview in Leopard (Mac OS X 10.5) now supports image markup, extraction and rotation.

Presentation:

• Keynote, part of Apple's spectacular iWork suite ($49 academic, also includes Pages and Numbers), will open and save presentations in the PowerPoint format. However, its ease of use, clarity of text, and facility with images and other multimedia leave PowerPoint in the dust. Step into a world where presentations don't put everyone to sleep!
• NeoOffice (above) has a PowerPoint-like module, as does Microsoft Office for Mac.

Screen capture (for creating video tutorials):

• iShowU ($20) is designed for creating video tutorials. It supports voice recording, screen capturing, drawing on a Wacom tablet, etc.
• Snapz Pro X ($69) is a professional-quality screen capture app that records full motion video and audio.

Drawing and Painting:

• ArtRage 2.5: A powerful Paint program at only $25, with a free lite version.
• Lineform: Use Lineform to draw about anything that Adobe Illustrator can do, but more easily, and it's much cheaper ($59 academic). Apple Development Award winner, August 2006.
• Omnigraffle: Premier flow-chart and diagramming application; a lite version comes free with Apple PowerBooks and MacBook Pros ($79).
• Comic Life: Quickly transform any photos or drawings you have into cartoons; included free on most Macs.

FTP

• CyberDuck, free, and surprisingly good -- for example, supports Applescript.
• Panic software's Transmit ($29.95) offers many more features, including remote editing, synchronization, column view, batch downloading, etc.

RSS

• Safari, the default web browser for the Mac, supports RSS subscriptions.
• This video explains why rss subscriptions are helpful.
• NetNewsWire is a superb rss reader for Mac OS X. Download the trial and you'll see how much more productive rss reading can be on a Mac! There's also a free lite version. Here's a review.

Miscellaneous

• Handbrake: Free utility to convert DVDs to QuickTime or mpg videos. Resulting videos can be edited in iMovie to produce the excerpts you want for playback in a Keynote presentation or on an iPod or iPhone.
• Reunion ($99): Fantastic geneaology software; I know people who have switched to the Mac just to use Reunion.
• Moneydance ($30): Personal financial manager that offers an impressive alternative to Quicken. Unlike Quicken, Moneydance supports multiple currencies and OFX standards.
• Parallels is a great facilitator if you have an obscure app that requires Windows; Screencasts Online has a video tutorial on how to use it. (Click the red button for a low resolution free version of the video tutorial.) But you may find that you don't really need Windows after all.
• Do you need dictation software to transcribe your voice into text? The main transcription software on Windows is Dragon Naturally Speaking, and it gets rave reviews. As of 2008, the same speech engine has become available on the Mac in MacSpeech Dictate. See David Pogue's review (including a short video)..

Scheduling

• Task Management
  • To Do's in iCal and Mail (Mac OS X 10.5 Leopard)
  • Omnifocus ($50 academic). Highly recommended!
  • Things, from Cultured Code.
  • Merlin Mann, "Getting Started with Getting Things Done", 43 Folders
    • Merlin Mann, Inbox Zero (video); highly recommended
• Project Management
  • Merlin, by Project Wizards (145 euros); MacWorld review
  • OmniPlan ($90): for management of large projects.

Bible and religious text software:

Accordance is the premier Bible and ancient religious text software available on any platform. Introductory modules range from $39 and up to several thousands of dollars. Many scholars who study biblical or ancient texts in the original languages have switched to the Mac just to use Accordance, because of its integrated searching of lexical forms and other advanced features. It is also very usable for those working in English translations, with a superb Atlas, Timeline, and Photoguide. Check out the Standard and Scholars video demos. There is also an informative and practical Accordance blog.

 

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HSCI 3013. History of Science to 17th century Kerry Magruder, 2004-07 Search this course website Report typos or broken links

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