Category: Productivity and organization

How I use the Zotero reference manager for collaborative grants or manuscripts

Why Zotero?

Zotero is an excellent and free reference manager that is my go-to for writing grants and manuscripts. It has some very handy features, like word processor plugins, web browser plugins that will grab PDF versions of documents if available, and ability to share “group libraries” with collaborators. It has all of the standard features of reference managers, like auto-formatting of references to meet submission requirements, automatic renumbering of in-line references, etc.

There are some silly things about Zotero’s initial setup that are important to get out of the way. For example, you don’t necessarily need to have a Zotero account to use Zotero (or at least you didn’t when I used it the first time). Make sure that you read about how to get set up with Zotero under the “Zotero” heading on this page. After you do that, come back here and read on!

How to use Zotero for collaborative projects

Zotero works well with MS Word and Google Docs. Examples here are taken from MS Word, but are also applicable to Google Docs. The main difference between Google Docs and MS Word is that the web browser plugin is also the Google Docs plugin. MS Word has a plugin separate from the web browser plugin. Regardless, whenever you use a Zotero plugin (eg the MS Word, Google Docs, or browser extensions), you also need to have the Zotero desktop app open. You’ll get an error if you try to insert a reference into a document or snag a reference from PubMed/a journal website if the Zotero desktop app isn’t also open.

Organizing your folders (“collections”) and subfolders (“subcollections”).

In your desktop app, navigate to the shared library that I’ll send you. Make folders/collections or subfolders/subcollections in there to help stay organized. To make a new folder/collection, right click on the shared group library and click “New Collection…”. To make subfolders/subcollections, right click on that new folder/subfolder that you made.

I suggest making collections/folders by section of your document, and numbering them so they stay in order, so: “01 Introduction”, “02 Methods”, “03 Results”, and “04 Discussion”. If you are writing something that doesn’t follow a usual flow (eg an opinion piece), number/name things by the major sections in your outline. You can always rename these folders/collections and renumber them so they show up in order.

Now, within each of these folders/collections, make specific groupings of subfolders/subcollections by topic. For example, in the introduction, you might have a sentence talking about the epidemiology/population prevalence of hypertension, then the costs (eg DALY lost) of hypertension, then an overview of the pathophysiology of hypertension, then how some biomarker relates to blood pressure. I recommend having a subfolder for each of these concepts separately in the “01 introduction” folder. You can also order these with numbers or letters, but it also might make sense to keep them unordered if you aren’t sure of how the introduction (or any other section) will flow.

Now repeat this for all of the other subfolders. The results folder might be pretty thin because usually (for me at least) there aren’t many references in that section. For the “discussion section”, I recommend including the suggested sections from my “your first epidemiology manuscript” example under “Download” here. It’ll look like this when you are done:

Next: Grabbing citations.

You need to install the Zotero browser extension, and make sure that you have the Zotero desktop app open when you are grabbing citations. I STRONGLY RECOMMEND GRABBING JOURNAL CITATIONS FROM PubMed AND ONLY PubMed. (For textbooks, Google Books works quite well.) Zotero uses metadata from websites to populate the reference. PubMed’s metadata is pristine. Journal websites have metadata, but it’s inconsistent and often incomplete. So, stick with PubMed when grabbing citations.

The first step is to find your article on PubMed. Let’s say you want to grab the AHA’s statistical update document, and using Google you find it on the Journal’s website. Welp, that’s not pubmed so don’t even think about grabbing the reference from here.

Instead, highlight the title and search Google again, appending the word “PubMed” to the search. This will get you to the Pubmed listing for that article.

Now this is very important! Go over to your Zotero desktop app and choose the subcollection/subfolder you want this to go in. This will be in the Introduction/Population Prevalence of HTN subfolder. You’ll notice it’s empty.

Now go back to the PubMed page for your document and click the Zotero plugin button.

Now when you go back to the Zotero Desktop app, you’ll see that the AHA Statistical Update is now saved in your “population prevalence of HTN” folder. If a PDF is available through Unpaywalled (a separate service that’s integrated into Zotero that grabs free/legal copies of journal PDFs), then a PDF will be saved as well.

When you grab references, make sure to sort them into a specific folder along the way. You’ll thank yourself later.

Next: Inserting citations in an MS Word document

Open up your manuscript file in MS Word. Make sure you click/set your cursor in the place in your document where you want the citation to land. (I’m a “citation goes after the period and not before the period” guy myself.) Then, click the Zotero tab. (If you don’t see the Zotero tab, you might need to try to reboot, or manually install the plugin. See the “Setting Things Up/Zotero” section above.) Now, click the “Add/Edit Citation” button. If this is the first citation/reference you are adding to this document, you’ll be prompted to select a formatting style, just pick anything since you can always change it later (I like the American Medical Association one to start with). You won’t see this pop up when adding other references.

Now you’ll see the hovering Zotero window. This isn’t a part of MS Word, it’s actually the Zotero desktop app. Sometimes this gets lost among your various programs/windows on your desktop and you need to go find it, it’ll be under the Zotero icon on your taskbar on windows. Or Alt+Tab until you find it. Anyway, this allows you to find a citation by text search (ie, by typing in the author name or title), but if you select the dropdown menu here, you can use the “classic view” and manually grab citations from your subcollections/subfolders. I recommend adding citations through the classic view.

In the classic view you will see all of your subcollections/subfolders. Navigate to your subcollection/subfolder of interest and click on the citation that you’d like to insert and hit “okay”. Notice in the “Classic View”, you can select multiple references at the same time by clicking the “Multiple Sources…” button at the bottom.

Now your citation is in-line! See the floating “1” after the first sentence. But where is the Reference list? Let’s plop one in. I added a new heading for references in MS Word and we’ll add it there. Click on the line after your “references” header, go to the zotero tab, and click “add/edit bibliography”.

End product is below. This reference list will update while you insert references in your manuscript. The reference numbers will also update automatically as you go.

Microsoft OneDrive

This is through LCOM. Not UVM, not your personal account.

  1. Open the OneDrive on your computer and sign in with your LCOM credentials if you aren’t already.
  2. I’ll share a research folder with you. You’ll need to sync it with your computer. To do that, go to onedrive.com, log in with your LCOM credentials (firstname dot lastname at med dot uvm dot edu). After you log in, you’ll be on the landing page for OneDrive. Click “Shared” on the left column. Find the research folder and click on it. On the top bar click “Sync” and allow the OneDrive desktop app to sync. Now all of the files should be available offline.

Microsoft Word

Unfortunately, writing papers in Google Drive is a bit too onerous.

Stata

You’ll be using Stata unless you are proficient in another statistical coding package. UVM has an institutional subscription. You can download and install it from the UVM Software page, here. For this you will log in with your UVM (not LCOM) credentials. To download it, hit the down arrow (1) then download. After it’s installed, you’ll need the serial number, code, and authorization to activate it. That’s under “more info” (2).

<– Two steps to install Stata from UVM

Getting your grant below the page limit using built-in MS Word features

It’s just a little too long!

You’ve toiled on your grant day in and out for weeks on end, and despite chopping out loads of overly verbose text, it’s still over the length. It turns out that there are some built-in settings in MS Word to help you get below the length limit without removing additional text. This post is focused on NIH grant formatting but details here are relevant for most grants. This also assumes that you are already using narrow margins. I made up a 4 page ‘ipsum lorem’ document for this so I can give actual quantifications of what this does to document length.

Hyphenation and justification

I only just learned about hyphens from Jason Buxbaum in this tweet. Hyphenation breaks longer words across lines with a hyphen in the style commonly used in novels. Hyphenation will get you a few lines in a 4 page document.

Justification makes words reach from the left to rightmost extremes of the margin, stretching or compressing the width of the spacing between words to make it fit. Justification’s effect on length is unpredictable. Sometimes it shortens a lot, sometimes it stays the same, sometimes it’s a smidge longer. In my 4 page ipsum lorem document, the length didn’t change. It’s worked to shorten some prior grants, so it’s worth giving a try. (Also, try combining justification with different fonts, see below.)

Here is the button to turn on justification.

Personally, I like ragged lines (“align left”) and not justified lines because I find justified text harder to read. I have colleagues who really like justification because it looks more orderly on a page. If you are going to use justification, please remember to apply it to the entirety of the text and not just a subset of paragraphs for the same reason that you don’t wear a tie with a polo shirt.

You can try combining hyphenation and justification, though I’m not sure it will gain anything. It didn’t in my demo document.

Modifying your size 11 font

Try Georgia, Palatino Linotype, or Helvetica fonts instead of Arial

The NIH guidelines specify size 11 Arial, Georgia, Helvetica, and Palatino Linotype fonts as acceptable options. (Note: Helvetica doesn’t come pre-installed on Windows. It’s pre-installed on Mac.) There were not major differences in length in my aligned-left ipsum lorem document between any of the fonts when the lines were aligned-left. But, try combining different fonts with justification. In the ipsum lorem document, justified Georgia was a couple of lines shorter than any other combinations of aligned-left/justification and NIH-approved fonts in Windows.

Condensing fonts

Kudos to Jason Buxbaum for this one. You can shrink the space between your letters without actually changing the font size/size of the letters. Highlight your text then home –> font little arrow –> advanced –> spacing becomes condensed then change the selecter menu to 0.1 pt.

This change will give you a few lines back in a 4 page document.

I can’t tell the difference in the letter spacing before and after using 0.1. If you increase to a number larger than 0.1, it might start looking weird, so don’t push it to far.

A word of advice with this feature: If you are too aggressive, you might run amok with NIH guidelines, which specify 15 characters per linear inch, so double check the character count in an inch (view –> ruler will allow you to manually check). FYI: all NIH-approved fonts are proportional fonts so narrow characters like lowercase L (“l”) take up less width than an uppercase W, and a random sample of text that happens to have a lot of narrow letters might have more than 15 characters/linear inch. You might need to sample a few inches to get a better idea of whether you or not are under the 15 character limit. (In contrast, Courier is a monospaced font and every character is exactly the same width.)

Adjust line and paragraph spacing

Both line and paragraph spacing affect the amount of white space on your page. Maintaining white space in your grant is crucial to improve its readability, so don’t squeeze it too much. In my opinion folks will notice shrunken paragraph spacing but not shrunken line spacing. So if you have to choose between modifying line or paragraph spacing, do line spacing first.

You can modify line and paragraph spacing by clicking this tiny checkbox under home tab –> “paragraph”.

Remember to highlight text before changing this (or if you are using MS Word’s excellent built-in Styles, just directly edit the style).

Line spacing

As long as you have 6 or fewer lines per vertical inch (view –> ruler will allow you to manually check), you are set by NIH guidelines. The default line spacing in MS Word is 1.08. Changing it to “single” will give you back about and eighth of a page in a 4 pg document. Today I learned that there’s ANOTHER option called “exactly” that will get you even more than a quarter of a page beyond single spacing. Exact spacing is my new favorite thing. Wow. Thanks to Michael McWilliams for sharing exact line spacing in this tweet. I wouldn’t go below “exactly” at 12 pt because that gets you at about 6.5 lines per inch, which goes against NIH standards of 6 lines per inch.

Paragraph spacing

The default in MS Word is 0 points before and 8 points after the paragraph. I don’t see a need to have any gaps between a heading and the following paragraph, so set the line spacing before and after headings to be zero. Looks nice here, right?

Now you can tweak the spacing between paragraphs. I like leaving the before to zero and modifying the after. If you modify the before and not the after, you’ll re-introduce the space after the header. Also, leave the “don’t add space between paragraphs of the same style” box unchecked of you’ll have no spacing between most paragraphs.

Here’s the same document from above changing the after spacing from 8 to 6 points.

Looks about the same, right? This got us about 3 lines down on a 4 pg document. Don’t be too greedy here, if you go too far, it’ll look terrible (unless you also indent the first line, but then you run the risk of it looking like a high school essay).

Play around with modifying both paragraph and line spacing. Again, I recommend tweaking line spacing before fiddling with paragraph spacing.

Window/orphan control, or how to make paragraphs break at the maximum page length

MS Word tries to keep paragraphs together if a small piece of it extends across pages. For example, if the first line of a paragraph is on page 2 and the rest of the paragraph is on page 3, it’ll bring that first line so that it ALSO starts on page 3, leaving valuable space unused on page 2. This is called window/orphan control, and it’s easy to disable. Highlight your text and shut it off under home –> paragraph tiny arrow –> line and page breaks then uncheck the window/orphan control button.

This gives a couple of lines back in our 4 page document.

Modifying the format of embedded tables of figures

Tables and figures can take up some serious real estate! You might want to nudge a figure or table out of the margin bounds, but that will get you in some serious trouble with the NIH — Stay inside the margins! Try these strategies instead.

Wrap text around your tables or figures

Consider reclaiming some unused real estate by wrapping the text around tables or figures. Be warned! Wrapping text unearths the demons of MS Word formatting. For this example, we’ll focus on just wrapping text around a table to make a ‘floating table’. Below is an example of a table without text wrapping.

Right click on your table and select “Table Properties” then click right or left alignment and set text wrapping to around.

Adjust your row width a bit and now you have a nice compact table! But wait, what’s this? The table decided to insert itself between a word and a period! That’s not good.

When MS Word wraps text around a table, it decides the placement of the now floating table by inserting an invisible anchor followed by a line break. Here, there’s an invisible anchor is placed between “nunc” and the period. Your instinct will be to move the table to fix this problem, and that is the wrong thing to do. Avoid moving the table because the anchor will do unpredictable things to your document’s formatting. This is so well known to create havoc that it led to a viral Tumblr post from user laurelhach:

laurelhach: using microsoft word *moves an image a mm to the left* all text and images shift. four new pages appear. paragraph breaks form a union. a swarm of commas buzzes at the window. in the distance, sirens. Text Font Line

Moving tables is pointless in MS word because it doesn’t do what you think it does and you will be sad. Move the text instead. Here, highlight that stray period and the rest of the paragraph starting with “Mauris eleifend” and move it where that weird line break occurred after “nunc”.

There will be a new line break to erase, but the table should now follow the entire paragraph.

If you are hopelessly lost in fighting the MS Word Floating Table Anchor Demon, and the table decides that it doesn’t want to move ever or is shifted way to the right (so much so that it’s sitting off screen on the right), then the invisible anchor might be sitting to the right of the final word in a heading or paragraph. I recommend reverting the floating table to a non-text wrapped table to figure out what’s wrong and fix everything. Right-click the table and open up the “table properties” option again and change the text wrapping to “none”. The table will appear where the invisible anchor is and now you can shift around the text a bit to get it away from the end of a sentence. Now turn back on text wrapping. This usually fixes everything.

Note: I actually made the table intentionally insert between ‘nunc” and the period for this example. This was just a re-enactment so it’s not MS Word’s fault — this time. BUT this really happens. It’s very problematic if you have >1 table or figure on a page because the Floating Table Anchor Demons will fight with each other and your grant’s formatting will pay.

Shrink the font in your tables

The NIH guidelines don’t specify a font size to use in tables, just something that can be read. I typically use size 9 font.

Reduce cell padding in your tables

This is especially helpful for tables with lots of cells. Reducing the cell padding shrinks the white space between the text in a cell and borders of the tables. In contrast with the “save the whitespace” principle of lines and paragraph spacing, I personally think that less white space in tables improves readability. Here’s before, with default cell margins of 0.08:

Highlight your entire table and you’ll notice a new contextual ribbon with “design” and “layout” tabs appear. Click layout –> cell size little arrow –> cell –> options –> uncheck the box next to same size as the whole table then reduce the cell margins.

Here’s that same table reduced with cell margins reduced from 0.08 to 0.03.

Now you can strategically adjust the column size to get back some space.

Also note that you can also apply justification and adjust the line and paragraph spacing within your tables, which might also help shrink these things down a bit.

Did I miss anything?

If I did, shoot me an email at timothy.plante@uvm.edu!

Writing your first epidemiology scientific manuscript? Here’s a generic MS Word document to get you started.

Your first manuscript will be be very hard

The first manuscript you’ll ever write is probably best described as a ‘slog’. It’ll take 2-3 times longer than you expect. This’ll be from a few different reasons:

  • Unfamiliarity with typical structure
  • Lack of a structured approach to writing a first draft
  • Developing the analysis too late in the drafting of the manuscript (i.e., not as a first step in drafting)
  • Deciding the tables and figures to include too late in the manuscript (i.e., after completing the analysis)
  • Not knowing how to use MS Word’s advanced features that can help optimize drafting

Here’s a resource that can help

I developed this generic research manuscript over several years of slogging through first drafts of epidemiologic manuscripts. It attempts to address the common problems and includes recommendations for the first drafts.

Here’s what it contains:

  • Page 1 – Helpful hints
  • Page 2 – Suggested steps to bring this to publication
  • Page 3 – ‘fill in the blanks’ cover letter
  • Page 4 – ‘fill in the blanks’ title page
  • Pages 5+ – ‘fill in the blanks’ for the rest of the manuscript

Download:

Click here to download (updated Aug 16, 2021).

I hope it helps!

Chrome extensions to help research productivity

Why use Chrome extensions?

Let’s be honest. Much of modern epidemiological research will be online, whether it be cruising PubMed, journal websites, learning introductory concepts on Wikipedia, or just straight-up Googling. You might as well optimize Chrome to help you surf for research in the most productive way possible.

Here’s a list of Chrome extensions that I have used and like.

Read Aloud: A Text to Speech Voice Reader

Have you used a screen reader before? Try it out! It’s especially helpful getting through huge blocks of text. There isn’t a perfect text-to-speech (TTS) extension yet. The closest is Read Aloud. Highlight the text to be read, right-click, and select the Read Aloud option.

Zotero (my favorite reference manager)

If you haven’t already committed to a bloated, high-cost, litigious reference manager that rhymes with “spend smote”, I’d recommend checking out Zotero. It’s an excellent, free reference manager with a very slick Chrome plugin. Just navigate to the PubMed page for a journal article of interest and click the Zotero Chrome extension’s button (you’ll need to have the Zotero desktop app open at the same time) and it’ll pull the full reference AND PDF if it’s available using Unpaywall.

Get Zotero here and the Chrome extension here.

Unpaywall: Direct linkage to freely-available PDFs for manuscripts

Unpaywall is brilliant. So brilliant, it’s integrated into Zotero. It indexes legal, university- and government-hosted PDFs for journal articles. If you’re on a journal’s website, you’ll see a grey or green lock appear on the right-hand side. If it’s green, just click on the lock and it’ll download the PDF from wherever it’s hosted. I bat about a 50% average of getting paywalled PDFs using Unpaywall.

EZProxy Redirect

UVM uses EZProxy to provide off-campus access to subscribed journals. If I wound up on a paywalled journal article that UVM has access to, there was a multi-step process of navigating to the library site, logging in through the proxy, and searching for the journal.

EZProxy Redirect automates that whole process. While you’re on a paywalled article’s site, just hit the button and it’ll bring you to the proxy access login then bounce you back to the article page with full access. It’s super easy. You just need to configure your institution once by right clicking on the icon and clicking Options. Note, this extension only works if your institution uses EZProxy. You can check the EZProxy database to see if your institution uses it.

Right-Click Search PubMed

Want to do a text search in PubMed? Just highlight the text, right-click, and select the “Search Pubmed” option. This extension simplifies searches for text.

MS Word’s new Read Aloud feature: Helpful for dyslexia and typo-finding

New in MS Word 365 is Read Aloud. It’s a pretty straightforward, stripped down/simplified text-to-speech (TTS) tool. If you have dyslexia or otherwise are having a difficult time finding typos in your work, try this feature. It’s very helpful.

To turn it on, just head over to the Review tab and click on the Read Aloud button.

It’ll automatically start reading from your cursor forward. Traditional icons for audio playback will float in the top right corner of your document window. These include play/pause, skip back (one paragraph), ad skip forward (one paragraph).

There is an icon of a dude with radio waves coming out of his head. That’s the settings button.

I like cranking the speed up by a few notches. You can also switch to other installed voices. I’m a fan of David’s sonorous speech. I’d totally pay a few bucks to have a Gilbert Gottfried voice though.

What if you have an older version of MS Word? Well, before this feature was released, I was using WordTalk v4.3. It’s a free, standalone app from the folks at the University of Edinburgh. It has some nice keyboard shortcuts that you can enable. The interface is very klunky though. In a pinch, it’ll do the trick.

2017-09-28 update

After using Read Aloud consistently for the past month, I still enjoy and recommend its use. However, I find it to be a bit glitchy with documents that have many co-author comments or embedded references from Zotero. In these documents, the playback will stop mid-word on occasion.

There are also some keyboard shortcuts for Read Aloud, documented here:

  • CTRL+Alt+Space – Start or quit Read Aloud
  • CTRL+Space – Play/pause
  • CTRL+Left arrow or CTRL+Right arrow – Skip back or forward a paragraph
  • Alt+Left or Alt+Right – Decrease or increase reading speed

2017-11-08 update

I received a new computer that ships with MS Office 2016, not 365. Read Aloud isn’t in Office 2016. It turns out that you can enable the older Text-to-Speech functionality in a pinch. If you don’t have the MS Speech Platform installed, you can download it here.

First, right click on the ribbon and select “customize the ribbon”.

Next, make a new group under the Review tab. I called mine Speak. Then under Choose Commands From, select All Commands. Scroll down to Speak and add it to your new group called Speak. Hit save.

You should now have a Speak button on your Review tab. Highlight what you want it to read and click Speak. Click it again to stop the reading.

You can adjust the reading speed under the Windows Control Panel –> Speech Recognition –> Text to Speech (on the left).

Keeping your digital work organized

I’m not an organized person by nature. However, I’m the kind of guy that likes to implement systems to overcome problems. In medical school, I didn’t have any sort of structure for my projects and found it frustrating to find the most recent versions of papers, posters, and other writings. Here’s an approach that I started using in fellowship that works for me.

Step 1: Save all of your work in one folder

This seems pretty obvious, but modern operating systems, cloud-based storage systems, and network drives all compete for your documents. If you are a windows user, I’m willing to bet that you have different projects saved on the Desktop, in your My Documents folder, in your cloud storage, and in your email in/outboxes. You probably also have alternate working drafts of your writings on different computers. This is a recipe for disaster.

Instead, make one folder that is accessible from your usual workstation. Call it Work, or something more creative. Save freaking everything in your Work folder from now until the end of time. 

Step 2: Make subfolders for different types of your work

Within your Work folder, make a subfolder for each flavor of project that you do. I have individual folders for Grants, Editorials, Non research (for blog posts and other miscellaneous work), and Research.

Step 3: Numerically and descriptively label each of your projects in its own sub-subfolder

Let’s say you are about to have your first meeting for a new research project studying the effects of Fro-yo vs. ice cream on cholesterol among adults. All of the relevant documents for your next research project will now be saved in the 001 froyo ice cream folder, seen here:

(You also had a good idea for a maple syrup study that you have also started simultaneously.)

What is the threshold to start a new numerically and descriptively labeled sub-subfolder? Mine is pretty low. If I think I have at least a marginally good idea and have started emailing folks about it, I go ahead and start a new folder. A PDF copy of those initial emails are often the first things that I save in that new numerically and descriptively labeled sub-subfolder. (I loathe MS Outlook but have to use it. Its search is terrible. Saving copies of important emails saves me some headache.)

What kinds of things are you going to save into these folders? That’s up to you. I recommend saving your literature searches, copies of relevant important emails, research proposals, and so on. I like to make sub-sub-subfolders with headings like Data and analysis, Manuscripts, PDFs (for relevant literature saved from your library’s journal subscriptions), and Presentations. You should probably number these folders to match the overall sub-subfolder number as well.

Step 4: Name each item within your sub-sub-subfolders starting with the a) sub-subfolder name, b) a short descriptor of the thing you are writing, and c) ending with a revision and version number 

Example: You finished all of your awesome dessert-related research and are starting to write up the main findings. You are going to start your first MS Word version of the first draft. I suggest naming it like this: “001 froyo ice cream main findings r00 v01.docx“.

Using version numbers

The r00 (that’s r zero zero) means that this particular draft has never undergone a major revision from a prior draft. The v01 (that’s v zero one) means that it’s the first version ever. You’ll email out a file titled:

001 froyo ice cream main findings r00 v01.docx 

…to your primary collaborator who will send back something with edits, they’ll probably save it as:

001 froyo ice cream main findings r00 v01 BHO edits.docx

…which is nice but doesn’t help with your naming structure. Immediately save that to Work\Research\001 froyo ice cream\Manuscripts\ as version 02, or:

001 froyo ice cream main findings r00 v02.docx

Accept or refuse their edits and save that version as:

001 froyo ice cream main findings r00 v03.docx

…then send this out to more collaborators. You’ll wind up going through somewhere between 5-20 (or more) manuscript versions before you are ready to submit to a journal. What’s nice about this system is that you’ll have no problems figuring out which version of a file you are getting edits on. Remember, at >5 collaborators, the probability of one co-author checking their email <1 time per month approaches 100%. You'll be working on the 10th version of your draft and receive an email from the slow reviewer with edits to version 03. Sticking to this scheme helps you figure out how to integrate their suggestions into the current version by tracking the intermediate changes.

Note: I suggest using two digits (v01-v99) for the revision and version numbers rather than starting with 1 digit (v1-v99). This helps keeping files in alphabetical-numerical order when sorting in your file explorer. Computers aren’t smart enough to figure out that v12 doesn’t come between v1 and v2.

Using revision numbers

For some reason, the New England Journal of Medicine doesn’t accept your manuscript for publication after sending it out for review. Lucky for you, it was sent out for review and the reviewers gave you some high-quality feedback that will improve your paper. Now it’s time to start revision 01! When prepping it for the inevitable JAMA submission, you’ll be working starting on revision 01 and version 01, or:

001 froyo ice cream main findings r01 v01.docx 

In the end, you’ll have a folder looking like this:

Look at how pristine and well-organized this is!

Step 4.5: Use trailing letters for projects with multiple publications

Let’s say that you decide to write both a main findings manuscript and a subgroup analysis manuscript. How to stay organized? Just the 001 Manuscripts folder into two sub-sub-sub subfolders for each publication, with 001a for the main findings and 001b for the subgroup analysis. It’ll look like this:

The naming scheme changes slightly as filenames will start with 001a instead of 001, like this:

Step 5: For the love of all things decent, regularly back up your Work folder!!

I can’t stress this enough. Keeping your Work folder in a commercial cloud storage drive doesn’t count as backing things up. Dropbox only saves things for 30 days in their basic plan. If you aren’t actively backing up your data, you can safely assume it isn’t backed up. One dead hard drive in a non-backed up folder can mean months or years of lost work.

Remember to check your institution’s policies for determining your backup method of choice. If you are working with PHI, saving it on an unencrypted thumb drive on your keychain won’t cut it. If it’s okay with your data policies, I recommend buying a DVD-R spindle or a bunch of cheap thumb drives and setting a calendar date to write your Work folder to a different DVD-R or different thumb drive once per month (i.e., you should have this on a different thumb drive each month). Keep these in a locked, secured, fireproof area that is consistent with the policies of your organization. Better yet, keep them in multiple locked, secured, fireproof areas if possible. For bonus points, get an M-Disc DVD discs and compatible burner, which should be stable for >1,000 years, unlike the usual 10-20 years of conventional burnable DVD-Rs and CD-Rs.

Or, just speak with your friendly neighborhood IT professional about how your institution recommends backing up the data you are working with. Chances are that they have a server that they back up 3 times per day that you can just use for a modest price. It’ll be worth the sorrow of lost data and drafts.

Tomighty: The Java-powered Pomodoro app

I’m a big fan of Tomighty. I have installed and used it extensively for the past year. It’s a simple timer for use with the Pomodoro technique. It helps maximize productivity and focus.

How I use the Pomodoro technique:

  • Pick up a kitchen timer (like the ones crafted to resemble a tomato, or pomodoro in Italian).
  • Get one sticky note and a pen. Stick the note to the right side of your desk. On the top, write “Pomodoros:”, a line down write “To do:”
  • Close your email, put your phone on silent, and get away from all distractions.
  • Set the timer for one Pomodoro (25 min).
  • Work non-stop for that 25 minute span.
    • If a fleeting thought is vying to distract you during that timeframe (‘send this quick email‘, ‘remember to order some more pens‘, ‘double check that that meeting made it to my calendar‘, or ‘send that cute picture of my kid to grandma‘), jot it down on a sticky note for later.
  • When your 25 min is up, count yourself one Pomodoro on the top of your sticky note.
  • Set your timer for inter-Pomodoro time (5 min).
    • Do the simple tasks on your sticky note.
    • Say “BAM” every time you check one of those boxes on your to-do list.
      • Don’t worry about getting through them all in this 5 min span.
  • When that 5 min is up, start your next Pomodoro.

The idea is to maximize the amount of Pomodoros you do in one day, not the duration of time that you work. Aim to get 3 your first day. Try to get up to 8 a week later. Only have an hour of time to work on one day? Do two Pomodoros.

With this technique, you stop counting minutes and hours and instead focus on bite-sized Pomodoros. As the day goes on and you rack up Pomodoros, you have fewer distracting thoughts and more productive time. For me, watching the clock causes a mild, counterproductive agitation. I don’t have this response counting Pomodoros.

This system helps you optimize your 1. Productivity requiring extended focus (writing papers, etc.), and 2. Productivity requiring little focus of silly things that you are putting off for later (quick emails, etc.).

In my opinion, the only drawback of the Pomodoro technique is the kitchen timer. It’s not quiet. Unless you have an office with a door and walls with soundproofing or work from home by yourself, this timer will cause problems with neighbors. Its not-so-quiet countdown/clicking and jarring ring will annoy folks in libraries, coffee shops, or cubicle communities.

Tomighty is a Java-based applet that replicates the tomato timer, written by Célio Cidral Junior. It has a lovely countdown click and time’s-up ring. It’ll keep track of your Pomodoros. It’s free and open source and should work on any computer (PC, Mac, Linux) with Java. Though, not the stock version of Java. I have struck out many times trying to figure out the correct version of Java to install and use. Every time I figure it out, I say “I should write this down.” Then I don’t. Fortunately, there is beta version written in C++ for Windows that doesn’t require Java. Just save the folder on your desktop and run the executable.