Grant Writing on a Mac
As my grant writing has ramped up over the years, I've gradually brought my workflow over to the iWork suite and found it much more satisfying than in the Office world. Surprisingly, there are no resources on the internet providing tips and tricks for research grant writing on a Mac, so I thought I'd share the things that I use and how it gets me to the end product with minimal fuss.
I'd love to hear other people's approaches to this. I'm coming from an academic biomedical research angle with this. The fact that almost all grant agencies prefer PDF grants liberates Mac users from the MS Office World and makes integration with iWork very easy.
My workflows...
1. Word "processing" - First there was Word and almost all people are locked into this in academia. Pages came along and provides a much more Mac-like experience than the behemoth that Word has become. I still think that there are advantages and disadvantages to both. In the academic setting the biggest need for Word nowadays is in collaboration. While track changes does transfer between Pages and Word it is not without flaws. The biggest issue I run into as I pass a document back and forth is keeping embedded references in order (e.g. Endnote). So in alot of ways, unless all my collaborators use Pages, I have to keep a copy of Word around.
The writing geeks in the Mac community are migrating to Scrivener that I'm starting to use. It has alot of very interesting features including having a research folder embedded in the file and able to focus on subsections when you write. Very interesting and liberating in many ways. Mac-only and does not track changes very well which makes collaboration hard but does permit saving versions which I find helpful as I rewrite sections of grants. It will import Endnote refs as text tags so will ultimately have to be formatted out to Pages or Word.
I try to stick to Pages to put the grant together. I'm starting to use Scrivener for the text creation initially. Google docs are intriguing way of collaboration on documents as well but the open nature of putting unpublished research out there is a bit scary.
2. Fonts - Here is a weird thing that I found. With the same document set up with via NIH guidelines with 0.5" margins and Arial 11pt - in Pages I get an extra line of text per page. This is within the NIH guideline for lines per page but it's bizarre. What I found is that Arial 11 in Word has a bit more space between lines vs Pages. In this world of shrinking grants...that extra line is kinda huge.
3. Reference management - Up until a year ago or so this was not easy to do with Pages which was a bit of a deal breaker but now Endnote X3 and the latest Pages play nice together. This was the final straw in me completely ditching Word for grant writing. I still find the Endnote integration buggy at times but it does work. I don't use RefMan or other systems to know how well they play nice with Pages. All of these programs can format the refs from an rtf file so that is the simplest default.
4. Creation of embedded figures/tables in grants - Need I mention the eyeball-scratching, pain that it is to create floating text-boxes in a Word document. Need I mention the times where the #$%@ thing jumps from one area to 6 pages away for no particular reason. Need I mention how awesome Pages is in rendering the documents and moving text boxes around.
Here is my workflow for creating embedded multipart figures. I'm adept at Photoshop and Illustrator but I found that this is the simplest overall once I have all the pieces in place.
1) Use Keynote to make the figure as a slide
2) Select the portions that I want in the figure and copy to clipboard (apple-c)
3) Open Preview and select new file from selection (apple-n). This creates a new preview window with my Keynote selection
4) Select the area I want to include in the figure and copy to clipboard (apple-c). This lets me trim to maximize space. You can also crop and save this as a jpg/tiff or whatever.
5) Go to Pages, make a text box, paste the selection into the box and resize as you want. Text can be added below the figure or on the side if you set the box to have 2 columns.
I'd love to hear if people have a quicker way to do this. Pasting from keynote directly doesn't work. If I want to edit a figure in the grant it's very quick. This is in contrast to opening illustrator, edit, save the file, reimport the file into Pages. I have a keynote doc that has all the figures for each grant.
5. Creating graphs - I don't use Numbers at all as they didn't have error bar support for the longest time (and its still not perfect). Excel stinks at compatibile graphs IMHO. I use Prism (our school has a site license) which is very powerful. There is a bit of a learning curve but graph creation is really straightforward and it works.
6. Putting it all together - Just print to a PDF and you are done from a Mac. Doesn't get better than that. Adobe Acrobat is still often required to merge PDF's and I find it the most consistent.
Those are my thoughts. I'd love to hear what other people are doing.
You can actually merge PDF
You can actually merge PDF documents for free using Preview under 10.6. Just open up each document in its own window and then you can drag pages from one document into another in the sidebar. Then do a save as to save the merged version and keep the originals intact. I use that feature all the time to tack SOM onto the end of articles in Papers and haven't run into any problems so far.
Interesting, I'm in the same
Interesting, I'm in the same field and have a near-identical experience and workflow.
1. Love Pages, but have to keep MS Word around for forms that I receive in MS Word format. I used to use Scrivener a couple of years ago, I though it was great until I had a few urgent requests from collaborators to get a draft of papers I was working on - it was embarrassing how difficult the process was to produce a reasonably formatted draft quickly in Scrivener, and others mentioned as much. It made me realise I was overcomplicating things and switched to Pages.
2. I noticed this too. I also found the fix, but can't remember right now what it was! It was something very general though like header size or ligatures or something.
3. Also agree that Pages seems to screw up Endnote citations when they go back to MS Word - hope Apple can fix that one.
4. I'm also good with Illustrator, but found that the drawing tools and bezier curves in iWork to be pretty darn nice and efficient. They are limited though. Would love to see Apple expand the capabilities with slicing paths, etc to let me ditch Adobe.
5. You mist learn Numbers. I'm an Excel guru including VBA programming, but Numbers is slicker in so many ways. It looks deceptively less powerful than it really is. I'm glad though that the iPad version placed the tabs at the top, the tabs and icons at the side looks plain ugly.
6. Yes PDF support is great. I've had near 100% accuracy in the translation to PDF from iWork. The only exception is that some legends in Numbers don't appear when copying and pasting into preview. I find I need to paste in Keynote first then recopy and paste into Preview.
Yeah...I worry that
Yeah...I worry that scrivener makes things too complicated but it's a pretty awesome program.
Here's a question, do people find Papers that useful/powerful? I'm still on the fence about it and have tried demos a couple of times. It seems a bit pricey to me and I'm not 100% it's needed.
What do you think about
What do you think about inkscape in lieu of illustrator ? I like it a lot, but it's been a while that I used Illustrator so it is hard to judge its performance against it.
Papers is well worth it. It
Papers is well worth it. It really benefits though if you work on large or multiple monitors
I think once I tried the
I think once I tried the demos of Inkscape and a few other cheaper or free Illustration packages, but never bothered with them as I have a licence for Illustrator. My guess is that most scientists don't need all the features of Illustrator, so more nimble packages would suffice.
You can merge PDF's with a
You can merge PDF's with a LaTeX package called pdfpages, it is very flexible. But it seems you don't use latex at all. So you have to deal with all the problems around word processors.
Two main options as far as
Two main options as far as I'm concerned:
1. if the grant proposal requires one to fill in some MS Word .doc forms, as much as I love Pages (or even Neoffice in various cases), the forms in .doc files do not usually render well in Pages and the formatting is all messed up. This is the only reason why I actually purchased MS Office for Mac: filling forms in .doc files... (sad ain't it?)
2. for the non-form parts of proposals, I simply use LaTeX, which makes my life easier for references, etc . Pages would do in most cases, but I like the flexibility of LaTeX and am used to it. Note, if you are not a latex user but would like do have nice equations in your documents, I strongly recommend installing MacTeX and using LaTexiT. One can write equations and copy/paste them in various format (e.g. jpg) into any documents (e.g., pages, Word, etc). One can even use the LaTeXiT services straight from Pages and write equations in LaTeX format. The best invention of the past 35 years after Nutella.
I then first export the various docs (forms, actual proposals, etc) in pdf and combine them all using either Preview or PdfClerk is more work is needed.
For quick and reasonably decent graphics, OmniGraffle is my favourite app.
For references, I use Papers. I create a dedicated collection for my grant (or for any paper). I then export the whole collection (group) to BibTex. I then clean the whole .bib with BibDesk (remove URLs, etc) and voila, ready to use for my .tex proposal.
Nico
www.volcanoloco.org
www.gns.cri.nz
I've found Sente to work
I've found Sente to work very well with pages for references, especially for grant writing. You can control the spacing between lines in all word processing programs. They must just use different defaults. Arial I think traditionally was a microsoft font. Any time you can save a figure or graph from another program as a pdf vector graphic, it will look much better when you embed it in Pages.
I'm at the end of my 4th
I'm at the end of my 4th year of PhD program, and I've been using Papers for three years now -- I think it's the most useful program that I have installed, save for LaTeX. I don't have a clue how I would manage without it, and I use it for basically all literature-related research, from searches, through import, reading, to managing references. No dollar has been wasted for a license for it.
LaTeX! I completely agree.
LaTeX!
I completely agree. I have been writing all my grants with LaTeX for several years, and the new NIH submission process requires pdf documents for everything; there are no longer forms (for which we all had to buy Word).
Obviously the Pages approach aims at making the user experience smoother than Word but preserves the constant in your face appearance of the document. Many people who use LaTeX talk about the liberation from worrying about what things will look like, I would simply emphasize that they are correct. It has enabled me to concentrate on the words and content without any worries about tables and figures jumping around, etc.
Earlier poster asked about Papers value and thought it was "pricey" - I believe it is worth its weight in gold and is very inexpensive for what it accomplishes. Keep all your references and PDF documents in Papers, take notes there, mark them as being involved in your grant, create a smart folder that looks for that "mark", and export the entire folder to Bibtex. Extremely convenient.
J. Michael Dean, M.D.
LaTeX or Pages or others, it
LaTeX or Pages or others, it is simply personal tastes. I use LaTeX to write anything and sometimes even plain tex. But I think Pages is a good balance between the entrance barrier and output quality. It is easier to learn than tex. Though the output won't be as good as tex, but is still far beyond acceptable. Word? It is just expensive, hard to use, and ugly output.
Great comments everyone.
Great comments everyone. Weighing in with my two cents.
Word Processing
I also like Pages much better than Word, particularly for its more intelligent handling of vector graphics, including PDFs. In Word (and PowerPoint), PDFs get rasterized which I find makes the file much larger and often leads to pixelated graphics when figures are resized or moved. I have even recreated the NIH's Continuation Page in Pages. The referencing software I use plays nice with Pages (see below) but it's not the best for collaborations.
Reference Management
I really like Papers and wish its referencing capabilities were more powerful. (Are you listening Mek & Tosj?) We don't get a discount on Endnote through my university, so I purchased Sente. I am really happy with it and the updates that have been provided recently. Because the reference finding/filing capabilities are mostly redundant with Papers, I have been using Sente almost 100% of the time.
Embedded Figures
Someone else mentioned it, but I'm a big fan of OmniGraffle. I find it more than sufficient for nearly all my figures. The one exception is when I have a figure with lots of lines, such as a number of contour plots from 2D NMR spectra. OmniGraffle seems to have a difficult time handling many curves and tends to throw the beachball quite a bit.
Regarding the issue with copying and pasting from Keynote, cbear44, have you tried grouping the items in Keynote before you copy? The last time I used Keynote to make figures, this fixed what I suspect is your issue with pasting directly from Keynote.
Creating Graphs
I can't say enough good things about DataGraph for lightweight graph creation on the Mac. The interface is nice, every aspect of the graph output is customizable, and you can create templates so that graphs can be created in batch from scripts. It doesn't do really complex fitting, but I usually switch to Matlab/Octave/Python for that.
PDF Management
I have always merged PDFs using Preview. When I have to fill out PDF forms, I use PDFClerk Pro. This is another piece of software with which I have been thrilled, and at $44, it's a fraction of the price of Adobe Acrobat Pro.
Cheers
Michelle Gill
I've learned alot from this
I've learned alot from this thread...thank to all for providing their tools of the trade.
Michelle, for some reason grouping doesn't bring all the elements from Keynote to the clipboard as a set. I love Omnigroup products (Omnifocus and Omnioutliner user) and have heard alot about Omnigraffle...I'll have to check it out again.
Latex is really intriguing and I had looked into this many years ago. WYSIWSG is my current comfort zone. It looks like a few things that I need may be slightly tricky and I'd have to invest effort in figuring out (e.g. superscript, subscript in text, embedded) Which text editors do people recommend that may have Latex plugins? Textmate?
That being said the other tool that I rely heavily on for writing is Textexpander and I could see implementing this well with Latex.
Carey Lumeng MD PhD
LaTeX vs Pages
LaTeX vs Pages
As a LaTeX heavy user (since well, more than 20 years now) I always write my scientific reports or grants with Pages (since it exists). If I need to include real math I just drop a dpf. Moreover, this separates the general discussion from the real math content. I keep LaTeX for the real work, where it is irreplaceable: writing papers or books. Pages is much more flexible and simple and we don't need all the LaTeX packages to colorize text, put this font or the other one etc... Things that Pages does for you simply and for free.
BTW what I miss the most would be an integration of LaTeX in Pages, but this is another story.
Good luck.
Given the discussion of
Given the discussion of using LaTeX this link might be of interest
http://chachatelier.fr/programmation/latexit_en.php
Sorry that grouping in
Sorry that grouping in Keynote didn't work for you, Carey. I just checked an old Keynote figure and it worked for me, but maybe my figure happened to only use elements for which grouping works.
I really like LaTeX for typesetting equations. The combination of TeX FoG and LaTeXiT (the later of which is mentioned a few posts below) are good for creating a GUI-like environment (similar to MathType, but free/donationware) for equations.
The link to LaTeXiT is a few posts below. Here is the one for TeX FoG: http://homepage.mac.com/marco_coisson/TeXFoG/index.html
LaTeXiT has a service menu item that will insert equations into Pages/Keynote/etc. You will also need a working TeX installation. I suggest Basic TeX if you just want to try out TeX FoG and LaTeXiT: http://www.tug.org/mactex/morepackages.html
Also, in case you haven't seen it, there is an excellent set of LaTeX-like abbreviations for Textexpander: http://smileonmymac.net/blog/2009/05/04/latex-math-and-greek-symbols
Cheers,
Michelle L. Gill, PhD
I have been using FrameMaker
I have been using FrameMaker for my technical word processing for many years, and it very capable and satisfactory. I am surprised it hasn't been mentioned in this thread. Alas, the Mac version is discontued, so I have to use my trusty old Pismo to use it efficiently, and it will never work on Intel Macs.
I have been looking for a good replacement for ages. MS Word is not an option. Pages has a lot of strange quirks (I find it very counter-intuitive, which is not what I should feel about an Apple program), and is lacking many important features. I understand that you use some additional program for references handling. So far so good, but how do you write formulas?
I have also tried a bunch of third party offerings, but most are dull letter-writing junk that mimick MS Word.
LaTex was never my style, but I will give LyX a shot.
Has nobody ever tried the
Has nobody ever tried the combination of Mellel for writing and Bookends (instead of Endnote) for reference management?! It s cheap and powerful. In fact, I also throw in Papers, which is just the nicest way to keep your literature organized and with the simple "Send to Bookends" command, there is no problem in using it in parallel to that reference manager.
I use Papers for download
I use Papers for download and management of all papers. I use BibDesk to keep a large database of literates. The problem with Papers is that it only support the "article" type of publication to export to bibtex format. So I have to keep all other type of publications directly in bibtex form. I also use Bibtools and some other command line tools for manipulation my bibtex database. With some limitations, Papers is still the best way for management papers I have ever seen.
Hi all, I'm just starting
Hi all,
I'm just starting my PhD this year and I've been trying to reorganise and re-set my workflow because I've found out that after my honours, I can't find articles that I want and my notes are all over the place! With 100s of journal articles now, I can't remember what paper was important and why anymore and its creating a lot of extra work for me to re-read some of the journals. I've learnt quite a lot from this post and from the comments, and I would like to share my experiences with some of the programs mentioned here and perhaps ask a few questions as well.
Regarding the creation of figures with Keynote, what I do is to Export the particular slide (which usually comes out as a tiff image), then open it with Preview to crop it to size or do whatever editing is needed. Maybe this might work for you guys? The only problem I've had is that sometimes I make the figures too big in Keynote and it isn't as sharp anymore when it's pasted into Mellel (which I use instead of Pages; Mellel doesn't really handle images as well as Pages though I think, so this problem might not happen in Pages).
I've never tried using Pages for really long documents yet (I've been too scared to), is it buggy with large documents like 100 pages or so? I've downloaded LaTeX but I haven't got down to learning it yet. I do wonder though, is LaTeX a bit of an overkill for me to learn when I rarely need mathematical equations?
I really do like writing in Scrivener though, something about it just makes it nice to write in, and DataGraph is awesome for simple graphs. I haven't actually heard of anyone doing a Scrivener-LaTeX combination. Has anyone tried it?
I've used Sente for about 2 years now, and its quite good. BUT, it has some small flaws and bugs here and there. And after a certain accumulation of these bugs, I've decided to move to Bookends instead. It might not do as many things as Sente (e.g. PDF annotation like highlighting within Sente itself), but I feel that Bookends is more straight forward and less buggy [I've only used this for a couple of weeks though, so who knows?].
Does anyone use DEVONthink in their work flow? I'm still considering it and wonder if I REALLY need the AI searching function or would another program like Papers be better for storing and managing notes and journal articles for future writing?
Oh by the way, I use Preview to read and highlight my PDFs as well. The only thing is that all the annotations get saved into the actual PDF file, which some people might not like. I've used Skim before as well, but I'm not sure what advantage it has over Preview at the moment.
Programs I have: iWork'08; Scrivener; Mellel; DataGraph; Bookends; Notebook
It is not an overkill for
It is not an overkill for you to learn latex even you do not need mathematics. Latex is good for any writing that requires more structures than visual effect, which is almost always true in academy. But there surely are situations make learning LaTeX become an overkill, but I don't think that is about mathematics. If you ever had any experience of Markup languages, I assure you that LaTeX will be the easiest to learn among all markup languages (But programming with it, or more precisely, programming TeX, is totally another story. However most users never need to program TeX).
Regarding Skim, the only advantage I found it over Preview is the support for pdfsync. But that is only a benefit for LaTeX users. In short, with Skim, one can find the place in a LaTeX source file corresponding to a particular line in the output PDF, and vice versa.
Yep, I have to agree. Mellel
Yep, I have to agree. Mellel + Bookends on the Mac is the best combination I've found for grant writing and manuscript preparation. Mellel has a bit of a learning curve, but coming from a Framemaker and Latex background, its approach to structured document preparation was quite straightforward for me. I have yet to find any reference manager that rivals Bookends when paired with Mellel. I use LatexIT to create pdf's of equations and Matlab to create pdf's of maps, graphs, etc. and lay these out in Mellel, which autonumbers figure and table captions not unlike Latex. A very inexpensive solution, Mellel has its own text engine which even beats that supplied by Apple's OS.
Dave
Ah, at last someone who has
Ah, at last someone who has used FrameMaker! Dave, how would you feel about your Mellel+Bookends solution, from a FrameMaker perspective? I don't fear the learning curve; FrameMakes is pretty complex too, and as long as I am learning a tool that I have any hope for, I have a reason to stick to it for a while. Is Mellel powerful and flexible in things like cross-references and numbering styles? How about moving an old manuscript from Frame to Mellel? Like, a 600 pages book manuscript?
But you say that Mellel can't do equations at all? That sounds like a drawback to me. It makes me think of the messy solution I had before FrameMaker, building equations in separate tools an pasting them in.
I have used Pages for my latest papers, but it only makes me frustrated. It is totally counter-intuitive, and although it has a few more features than first meets the eye, it has an awful tendency to make the wrong decisions for me.
Yes, Mellel+Bookends is
Yes, Mellel+Bookends is highly flexible/customizable in terms of formatting figure/table captions, bibliographic references, etc. Not unlike LaTeX, you can set up a document style that formats your content according to, say, a specific technical journal's requirement. This specifies fonts, auto-numbering of text sections, figure/table numbering and captions, cross-refefences, in-text citation of bibliographies, formatting of bibliographies in the references section, auto-generation of TOC's, etc. If you decide to change journals, just apply a different document style and the formatting of the content is updated.
A month before I submitted the final version of my 200+ page dissertation, which contained LOTS of pdf figures and equations and 20 pages of literature citations, I moved it from Framemaker on Windows to Mellel+Bookends on OS X. It was WELL worth the effort as subsequent small editorial changes which needed to be done FAST were quick to implement. I'm sure there was a better way to do it, but being new to OS X, Parallels, and Mellel back then, I just used the clipboard to cut-&-paste the text from FM to Mellel, moved the PDF's from Parallels to OS X, and added the appropriate links to them, not unlike Framemaker. Mellel+Bookends handles literature citations MUCH better than Framemaker or LaTeX/BibTeX in my opinion. I've set up a Style set in Mellel that mimics the standard LaTeX article format and've even installed the freely available Latin Modern roman fonts, which makes great looking grant proposals.
No, Mellel doesn't do equations but I don't think ANY program comes close to what LaTeX does in that regard. Just install the free LaTeXIt program, type in your equation code, render it as pdf, drag to Mellel (or Keynote for that matter) and you're done. Save the equation code in LaTeXIt's library if you need to access it later, make changes, etc.
Right now the only thing really lacking in Mellel, in my opinion, is line-numbering, which is needed for some peer-review journals submissions. The work around is document creation in Mellel, output as RTF, and import/edit in MSWord, etc. to number lines.
You can also pair Mellel with Sente instead of Bookends, but I haven't tried that yet. Getting my 1000+ reference database from bibtex/amsref to Endnote wasn't a big deal, then going from Endnote to Bookends via xml was even easier. Give these a try, the academic pricing in crazy cheap. Also, see the Mellel user forum.
HTH,
Dave
I have two requirements of
I have two requirements of any technical word processing that are frequently not met--
(1) Autonumbering of _everything_ including figures and their captions, and equations. Pages loses right out of the gate. Also, Pages has no "online" viewing mode but insists on wasting valuable screen space with page margins. Also, Pages screws up indented lists when importing .doc files. But when its features are appropriate for the task, Pages is absolutely gold.
(2) Smart figure placement. The long-lost and much-missed FullWrite Professional was aces at this. I have to beg ignorance about how current word processors handle this. I suppose Framemaker is great for this. By "this" I mean, say you mention Fig. 12 on page 20. Fig. 12 should be placed the top of page 20 unless this forces the mention to page 21, in which case Fig. 12 should go at the top of page 21. The situation gets a little messier if there is an additional figure reference to Fig 13, but the software should just do the right thing. Also, there should be an option to place Fig. 12 as close to its first mention as possible on the same page, but forcing it to the next page if necessary. Does Word do this? I know Mellel and Pages do not, and I would place bets against any other Mac word processor except _possibly_ Mathematica.
I love the Mellel feel and the brilliant way it puts so much power in an easy-to-use interface (but with a bit of learning curve).
I wrote a couple of papers a few years ago in the student version of Mathematica and was generally quite pleased with the whole process, given that it is a bit quirky (as is all of Mathematica). But I did not like having to give a freaking name to every equation which reminded me of the one time that I tried to use Word for technical stuff. But being able to embed things made within Mathematica was awesome. I currently have the Home Edition of Mathematica and am eager to try out its presumably updated word processor.
I'm also good with
I'm also good with Illustrator, but found that the drawing tools and bezier curves in iWork to be pretty darn nice and efficient. They are limited though. Would love to see Apple expand the capabilities with slicing paths, etc to let me ditch Adobe.
Michel G. Nisus not
Michel G.
Nisus not mentioned as excellent word processing? I am surprised!
For bibliographic softwares, my preferred are the following:
For those who can read (or at least decipher!) the French language, I posted several reviews on 6 different bibliographic softwares:
http://www.cuk.ch/articles/4375
I thing LaTeX or Pages or
I thing LaTeX or Pages or others, it is simply personal tastes. I use LaTeX to write anything and sometimes even plain tex. But I think Pages is a good balance between the entrance barrier and output quality. It is easier to learn than tex. Though the output won't be as good as tex, but is still far beyond acceptable. Word? It is just expensive, hard to use, and ugly output.
I completely agree.
Website Designers London
Web Design Agency
Google Docs is unbelievable
Google Docs is unbelievable for collaborative grant writing: you can't rely on the use of Macs from your collaborators. I have found Google Docs to be a pure pleasure to use for several reasons:
1) Everyone works on the same version at any time. This is pure bliss compared to the nightmare last minute day-of-submission email: "I modified this old version, why don't you merge the comments. I also fixed typos here and there..."
2) The comment tools are very good.
3) You can now share with people who don't have a Google Docs account. Again, with some collaborators who are not tech-savvy, this is great. Not everyone reads Macresearch.org
4) The docs are private
5) The Old google Docs has very good "Compare history", with full history on everyone. The new one sucks but this will be fixed. You can always for ce a creation of a google docs document in the old format.
Formatting is not great, but that is not critical: I still put everything together in Pages.app when everyone is done editing. Reason 1) for me seals the deal.