New on this forum, but not really new to Manuscript. I have paid for the app, and I am using it since about 12 months. I have used Papers for Mac quite a bit, and I am (as many academics) of the unsupportive sort when it comes to the monopoly from MS Word). So an App that promises to do things better, with an uncluttered interface, and helps when it comes to submitting a paper would be a win for me.
As stated in the title, I can proudly say that I have now my first paper entirely written , submitted, revised, and accepted using ManuscriptApp v 1.1.4. This is my 40th paper or so, so I am not a novice at writing papers. But it is the first submitted with Manuscript. And apprpriately, the paper was about new software that we developed for the isotopic community. So I am sympathetic with the developers of Manuscript App, as I know something about tracking issues and satisfying a demanding crowd. Now, was the process of writing the paper on Manuscript enjoyable? Was it easier than with Words? Read along, and you will know the good, the bad, and the ugly!
Writing the paper:
Writing the paper with Manuscript was easy and not an issue. The specific style template for the journal I targeted (Rapid Communication in Mass Spectrometry) was available which made life easier. The paper is full of equations, so I had to resort to the LaTEX equation editor. I must say, in this respect Manuscript is better than words, and gives a good control on the equations. Writing the text and adding equations was relatively painless. A few issues did pop up though. For instance, if you have inline equations, you cannot copy-paste the text around them and the equation together. Also, referring to equations is easy enough, for changing the style of the reference (for instance, stating "eq." rather than the full "equation" in the cross reference is not possible - or I did not find how to do it! But the writing was easy. Manuscript does well here, the developers have ironed out the horrible bugs from the earlier versions, that would crash periodically.
I used Papers for Mac for my reference management. I like it, this is why I gave Manuscript a chance. The referencing using Papers is straightforward enough, and works quite well. I can format things the way I want, and use the ready-made templates for my reference. One annoying thing is that I have duplicates and triplicates of the same papers in my references. So in the end, I have 3 times the same reference in my reference list. I know, my bad. But I am busy, forget what is in my reference list, and I don't see an easy way to look for duplicates in Papers. Not a major problem, but a hassle. Here again, Manuscript+Papers do reasonably well, enough that I could consider using this as my default app.
In theory, I love the idea of keeping my figures within the paper. So I went boldly forward and dropped my figures into Manuscript. Easy enough to create the figures, the captions, and even to put the figures at the end of the manuscript. Again, the benefit is that cross referencing figures (as in equations) becomes easy. Although again, it would be nice to have more control on how this cross referencing is done, i.e. use "Fig." instead of Figure, or use Figs. 2-6" instead of "Figures 2 to Figure 6", etc...
The real problem with figures came when I wanted to export them. There is simply no good way to export figures in Manuscript. In theory, you can select them and do an "Export selection". But it does not work. Or you can print a PDF, and extract them from the PDF. But again, that's a lot of work. Or copy-paste from Manuscript to another software, like Illustrator. But then, what's the point? So my first disappointment is that figure management in Manuscript is rather poor. Once the figures are in, they are pretty and nice to have in. But when the time comes to submit for publication, you better have an illustrator version of the figures you want to use (see submission and revision after this). Word does not do better than Manuscript, to be fair, it's worse. So Manuscript still wins in my opinion, but it's not yet a very satisfying solution.
Submission and revisions
Submission and revision was the most painful part of my Manuscript experience. In part this is because most journal will at some point require you to submit an MS Word file, and some figures separate from the main text. On a good note, Manuscript actually impressed me at the task of exporting the text to MS Word: even the equations were correctly rendered in word, and I could modify them. All the reference and formatting worked fine, this this was a truly painless job. Only issue was that the equation numbering was NOT exported to word, which required a lot of manual numbering in MS word. This is in part because word does not have a true numbering system for equations, you need to use a special form of caption for that. At least the call to equation in the text were still there, so I simply needed to change the 34 odd equations. Not too bad. The authors address after the title was incomplete, so I had to change this in Word, and I also had to clean up some of the references in word because Paper did not do a proper job at rendering them. No biggie.
The trouble began with figures. There is simply no way that the App can handle submitting figures the way a journal would want you too. In my dreams, Manuscript App would display the figures in your manuscript where you want them, but then you would be able to "Export for submission to the journal" and all the figures would be exported individually into a folder with a figure number, but no caption, and the text would be export as an MS Word document in the same folder, with all captions for figures included. This is the standard format for submission. Instead, because I relied on Manuscript to do my figures, I had to redraft them (mostly screen shots of the App, luckily) in Illustrator right before submission. There Manuscript is no better than MS Word, and there is a lot of room for improvement.
And then came the revision cycle, and I was asked to provide a tracked changes version of my MS word manuscript. Not great, because Manuscript does not do track changes. So I circumvented the problem by exporting the original version to word, change it in Manuscript, then export the changed version to word, and compare the two documents in words (this gives me track changes capabilities). It worked. But it's very clunky, because it means that each time you change something, you need to change it in Manuscript, export to word, and redo the compare exercise. Not easy. Also, if you need to manually change something in word, then you need to do it at each export. In my case, this would have meant renumbering 37 equations by hand in word each time I changed something in the text. So I gave up at this stage, and stick to MS Word for my revisions because I did not have the time to deal with this. So in some ways, my first manuscript submitted with ManuscriptApp is really a hybrid, since Word was used in the end for the final product.
The App is usable, and I must say that I DO enjoy using it. I love the ability to mesh equations easily in my text, and I have the feeling of using a tailored App for scientist, not your mom's hand-me-down MS Word. But equally, and realistically, I am an overworked academic, and as many mentioned before, the App needs to be pretty solid and make my work cycle easy for me to work with it. Mostly Manuscript does the job, with a pretty good export functionality to Word, which is essential as a standard for submission. What is crucial in my opinion are the following:
- Implement the ability to track changes, and export those track changes to word
- Give more flexibility in the formatting of the authors, the title, references to figures, equations,etc...
- Not essential but probably something that would make a big difference in terms of adoption of the App would be the ability to export the Manuscript file for publication, i.e. generating all the required files into a folder, with figures exported individually and without captions in a format chosen by the user (PDF, eps, TIFF come to mind)
Will I keep using Manuscript? Yep, at least for a little while. I was, as many, disappointed by Paper2 when it came on the market. But the developers did a good job at listening to us, and producing an App that we like. I am betting on the fact that they will do the same with Manuscript (hence my review today: hint, hint). Also and to be fair, Manuscript is already 90% usable and enjoyable. The problem is that most of the target audience for this app is overworked, and cannot deal with the hardship of the remaining 10% that need improving.