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Old Jan 8, 2013, 02:13 AM   #26
ssmed
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I would use the program you are most familiar with and at the risk of teaching you suck eggs here are a few other tips based on rescuing a number of MSc and PhD students in extremis over the years. Do check with the college/university that they don't have a specific requirement for archiving, plagiarism checking or the examiners.
  1. Whichever work processor you use - buy/borrow a book as a reference (writing a thesis usually means you will need to increase your knowledge of the application)
  2. Use paragraph and character styles for consistency
  3. Use separate documents for chapters especially if there are many large images which appear to cause the most problems with corruption.
  4. If you use a reference manager such as Endnote, accurately enter the references - it will save you hours at the end.
  5. Back up ALL the time

If you don't like Word, you could look at Mettel, but this works with fewer citation managers.

HTH and good luck. SS
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Old Jan 8, 2013, 04:51 AM   #27
benwiggy
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I'm using Pages for my PhD. I've setup my own "Thesis" template, with styles for cited passages, footnotes, auto-numbered section headings, etc.
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Old Jan 8, 2013, 04:58 AM   #28
leman
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Quite honestly, I hope that OP successfully finished and defended his/her thesis, seeing how the original question was asked two years ago ^^

Personally, I do all the typesetting exclusively with LaTeX and urge all my students to do the same. Word processors are just too limited when it comes to math/citations/footnotes and other advanced formatting; and the output they produce is UGLY.

A nice way to work with LaTeX btw. is to write your documents with Pandoc multimarkdown
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Old Jan 8, 2013, 06:50 AM   #29
switon
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RE: Ahhh ... latex

Hi,

I concur with Professor leman and several others concerning latex. TeX produces beautiful "textbook" or "scientific article" output without the writer having to worry about the results -- the author gets to concentrate on the content with almost no thought going to the final output: it's going to be beautiful thus allowing both the writer and the reader to concentrate on the content and not on the formatting.

With the other tools that come with TeX, such as "makeindex" and "bibtex", you can produce a final pdf document that includes automatically generated Table of Contents, Table of Figures, Table of Tables, Bibliography (in any style you wish), and Index, along with numbered labels for all Chapters, Sections, Subsections, and Subsubsections and referenced numbering/labeling of any and all equations, tables, figures, footnotes, or enumerated lists. Did you ever wish to refer to a particular item/equation/figure/table/footnote and list what page it is on without ever having to worry about repagination after future edits?

That said, I don't know what microbiology as a field uses for its journals. They might use latex since there could be a fair amount of statistics included in microbiology papers and nothing else really comes close to the results of latex for equations in my opinion, but I would recommend that the OP learn to use what his/her field uses for its articles. In physics and mathematics, this generally means latex ... have a look at arXiv.org or the AMS to see that all physics and math manuscripts, and even quantitative biology articles, are delivered as latex source and their tex outputs such as pdf, ps, and even dvi.

Now for my caveat, I must admit to knowing very little about the current Word/Pages applications. Being an antediluvian troglodyte, a millennium ago I attempted to write a math-filled article in Word. Not only was the math extremely painful and time-consuming to write, but when the document got to roughly 50 pages Word just refused to continue (crashed). Now I'm sure that Word has gotten much better since my attempt, and perhaps even equations in Word have gotten easier and better, but that experience made me forever switch to TeX.

...and yes, I too note that the OP has long finished his/her Masters thesis...

Regards,
Switon
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Old Jan 8, 2013, 12:20 PM   #30
benwiggy
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I certainly hope that the OP's Masters has been finished!

My one criticism of LaTex is that everything it produced looks like it's been done in LaTex. That may be desirable in some quarters, of course.

My supervisors want to use Word's "Commenting" feature to comment on my writing. However, I have to use many in-line vector graphic examples, which Word handles poorly.
Pages is a doddle to set up with a template of all the necessary styles.
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Old Jan 8, 2013, 12:32 PM   #31
ssmed
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Quote:
Originally Posted by benwiggy View Post
My supervisors want to use Word's "Commenting" feature to comment on my writing. However, I have to use many in-line vector graphic examples, which Word handles poorly.
You can get around this when not using Word if they have Acrobat which can be used to mark up with comments and allows easy emailing of otherwise large documents.
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Old Jan 8, 2013, 02:08 PM   #32
switon
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RE: the LaTeX look...

Hi benwiggy,

Yes, if by "it's been done in LaTeX" you mean "practically perfect in every way", quoted from Mary Poppins I believe, then I agree that LaTeX output is easily distinguishable from the output of Word/Pages and most other programs, especially with respect to mathematical formulae.

At the same time, TeX does allow for a number of "formats" or "documentclasses" or "styles" that allow you to change the 'look' of the document, including how things are formatted and labeled, without having to change any of the content. For instance, the American Mathematical Society (AMS) has their own 'look' by providing their own "documentclass".

Benwiggy, what if you used LaTeX and then gave your supervisors the PDF files generated by LaTeX that they can make their comments on (using any number of apps for such a purpose). Your supervisors make notes in the PDF and email it back to you and you then incorporate any edits into your LaTeX source. The reason I suggest this is because LaTeX also does such a nice job with incorporating vector graphics that this alone might be a reason for using it.

By the way, may I ask what program you currently use to generate your vector graphics?

Regards,
Switon

Last edited by switon; Jan 8, 2013 at 02:46 PM.
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Old Jan 8, 2013, 03:48 PM   #33
benwiggy
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Yes, the more technical of them write comments in Acrobat on PDFs. The rest use red pen.

My vector graphics are created in Finale, as they are music notation examples.
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Old Jan 8, 2013, 03:56 PM   #34
dukebound85
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I am using word as that is the program I feel most comfortable with

Last thing I want to do is learn how to use a word processor at the moment

----------

Quote:
Originally Posted by ssmed View Post
I would use the program you are most familiar with and at the risk of teaching you suck eggs here are a few other tips based on rescuing a number of MSc and PhD students in extremis over the years. Do check with the college/university that they don't have a specific requirement for archiving, plagiarism checking or the examiners.
  1. Whichever work processor you use - buy/borrow a book as a reference (writing a thesis usually means you will need to increase your knowledge of the application)
  2. Use paragraph and character styles for consistency
  3. Use separate documents for chapters especially if there are many large images which appear to cause the most problems with corruption.
  4. If you use a reference manager such as Endnote, accurately enter the references - it will save you hours at the end.
  5. Back up ALL the time

If you don't like Word, you could look at Mettel, but this works with fewer citation managers.

HTH and good luck. SS
1) Good idea, haven't felt the need though perosnally
2) Good advice
3) Yup, exactly what I do Each chapter is its own document
4) I hate managing references.
5) YES.I know for me, I have local copies on my work and personal laptop, each one then has a time machine backup. Each one is synced with dropbox. I will do a biweekly copy onto a flash drive, as well as having a carbon copy of my personal laptop hard drive. That's what? 7 backups over 3 locations

Learned the hard way

Only thing I don't have backups for is data as that is very space intensive. However, my scripts that manage the data is backup'd in the same manner as my thesis! Can always redownload data
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Old Jan 8, 2013, 09:50 PM   #35
ultraspiracle
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I finished my PhD thesis in microbiology last May using Word for Windows (Word 2007) which wasn't even the latest version of Word for Windows, and it was very stable. I would recommend Word for Mac, but here are some caveats.

On my mac, I have Word 2011. While it's fine for everyday stuff, it could be extremely unstable with "track changes" on and lots of endnote citations (you do plan on using EndNote, don't you?). I finished a grant writing fiasco late last year using Word 2011 and EndNote 5 for Mac. EndNote 6 for Mac with Word 2011 is no improvement.

OS X 10.8.2 and EndNote (any version) do not get along well at all - this is Apple's fault, since the problem only exists with 10.8.2 and not any other version of the operating system.

So, if Word is working for you right now, I would stick with that. With Pages, there are no cute shortcuts for introducing symbols (delta, sigma, lambda, etc.), and I dont' know how Pages would handle images from Powerpoint....I assume it would handle images from Keynote just fine, but again, Keynote does not have the features that many of us often use in Science, so that would make thesis writing with Pages/Keynote a real pain.

Take what you will out of this - there's no way in Hell I would use something like LaTex.
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Old Jan 9, 2013, 12:13 AM   #36
vistadude
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Why do LaTex fanboys say that Word users focus on making the document beautiful while LaTex users focus on the content. It's hard as hell to focus on the content when you have random symbols and \?n characters all over the place. Secondly you can't even see the images that you are writing about until you compile or print off a pdf.

Thesis and dissertations have to follow a format that your university, college, or department has set. Word users don't focus on formatting and making the text beautiful. They simply type sentences, insert images, and do the formatting, before or after the chapters are written. Heck, your advisor will need to add comments and no way in heck they can add hundreds of comments with PDF commenting and even lesser chance they know or want to figure out how to use LaTex. And yes, secretaries have to check the margins and indentations and can't do that with LaTex.

Use Word and EndNote or another citation manager.
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Old Jan 9, 2013, 03:47 AM   #37
benwiggy
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Quote:
Originally Posted by ultraspiracle View Post
OS X 10.8.2 and EndNote (any version) do not get along well at all - this is Apple's fault, since the problem only exists with 10.8.2 and not any other version of the operating system.
A likely conclusion, but by no means certain. Endnote may have been using deprecated or undocumented APIs which have been withdrawn.

Quote:
Originally Posted by ultraspiracle View Post
With Pages, there are no cute shortcuts for introducing symbols (delta, sigma, lambda, etc.), and I dont' know how Pages would handle images from Powerpoint.
Pages can deal with images very well. It doesn't care where they are from, as long as they are standard format. And IME, it handles images a lot better than Word, particularly EPS and PDF.
You can paste equations directly in from Apple's Grapher application.
But don't get me started on PowerPoint. As Edward Tufte famously points out, it encourages hierarchical relationships between data where no such relationship exists. It's also wrongly and over-used, though that's not the fault of the software itself. But I digress.

I think Word is pretty much the "default" choice and doesn't really need recommending -- For all its faults, it's ubiquitous, and is the de facto standard. Some people have difficulty grasping the concept of "another word processor than Word". Hell, my university has only recently stopped REQUIRING Office and Windows as compulsory for its students.
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Old Jan 9, 2013, 04:57 AM   #38
ssmed
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Quote:
Originally Posted by benwiggy View Post
A likely conclusion, but by no means certain. Endnote may have been using deprecated or undocumented APIs which have been withdrawn.
I am troubled by this bug. Endnote are very assertive that this an Apple problem (see http://community.thomsonreuters.com/...on/td-p/34965/). It had better be - as Endnote have a poor track of getting bugs fixed. There was a frequent, albeit intermittent bug, that meant that you couldn't tab between entry fields that was never addressed until the next paid upgrade a few versions back.

Endnote rely on a big university user base and the fact that users build up large, useful and highly personalised libraries. In the University environment I suspect that Windows machine predominate and that is their focus. They are also bringing out an iPad version in the next few weeks and one wonders whether they, like Apple, have been distracted by iOS.
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Old Jan 9, 2013, 05:28 AM   #39
benwiggy
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I've never really been impressed by these tools such as EndNote, EverNote, Mendeley, Papers, RefWorks, etc, etc. They're all either expensive, buggy, have poor user interfaces, or a combination of the above. I can't really see the utility in them.

Apart from organizing citations into one place, what do they do? I can't really see the need to spend 160 on EndNote.

I copy/type references into text clippings, which go in a big folder. I use Spotlight to access them. I have FileMaker for my main research data.
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Old Jan 9, 2013, 07:27 AM   #40
switon
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RE: Word vs LaTeX...

Hi,

As I discussed in my earlier post, I recommended that the OP should learn to use whatever tools are required for the journal publications in his/her field: those might be Word, those might be TeX.

(removed irrelevant material...)

Respectfully,
Switon

Last edited by switon; Jan 11, 2013 at 06:12 AM. Reason: Removal of irrelevant material...
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Old Jan 9, 2013, 07:39 AM   #41
Brian Y
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In the mathematical sciences, LaTeX is the *only* thing you should be using.

Biology is a different kettle of fish, however. It's a very verbose subject with little equations. I've seen a whole host of biology papers which have been written in word/similar, but relatively few written in TeX (the exact opposite of mathematical sciences).
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Old Jan 9, 2013, 07:43 AM   #42
klaxamazoo
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LyX is a great LaTeX GUI wrapper. It took a lot of the intimidation of using LaTeX away, shows Figures and Tables instead of just mark-ups, and make Table formatting much, much easier.
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Old Jan 9, 2013, 11:07 PM   #43
ultraspiracle
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I'd like to see someone these days write a 200+ page thesis with 150-250 references and curate it manually. It can be done, but it's masochistic.

Endnote (or similar), when it works properly, is the way to go. It puts your citations in, formats them correctly according to the journal you expect to send the publication to, and formats the bibliographic references. There are specific formats that are obtainable from most of the major scientific journals (they all have their own way they like references). The biggest help is that EndNote moves citations around in the text as you edit and doesn't lose the link to the bibliography. The only caveat is that you have to start with an endnote "library", which you can create yourself. Not much of a learning curve - several hours of preparation and you'll be good to go.

I can't imagine how I wrote a 100 pg. MS thesis without it, but that was back in the days before endnote. There would be no way I have the patience to do that again.

Last edited by ultraspiracle; Jan 9, 2013 at 11:13 PM.
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Old Jan 10, 2013, 01:10 AM   #44
vistadude
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Switon,

You make some good points, but let me refute a few things to your argument. I work in a physics department and have published in a few of the APS journals, so I am familiar with LaTeX although admittedly not a user. My groupmate uses LaTeX, and has shown me a few times. In his program or text editor, I see lots of weird symbols and it makes it hard for me to read what he wrote. Maybe that's his choice of text editor but LaTeX has no standard for this whereas Word looks pretty much the same on PC and mac, even versions 10 years old. About the equations, I have never seen inline equations in a journal or thesis, I have always seen them on their own line with spaces above and below. But then again, if the journal requires inline, the editor's office will take care of the formatting (You don't have to as a Word user), so there is little to worry about formatting. Also for equations, word doesn't handle equations as images, they are pasted as standard characters, so they are always easy to modify when copying and pasting.

Now I completely agree with you that APS and other physics journals request LaTeX (not require) because the text does look formatted better. And indeed it does speed up the time between acceptance and publication. I have seen proofs come 2-3 days after a manuscript is accepted when the authors used LaTex whereas people who use Word end up waiting 1-2 weeks. But that's simply the work of the editor's office. I have also seen groupmates who send their manuscript to collaborators in LaTeX or pdf don't get much feedback or suggestions because no one can figure out a good way to track changes or add commenting capability, whereas people in my group who use Word get a lot more help from co-authors.

Btw I didn't state LaTeX is worthless, it is actually great for editors offices, but for most users, Word is far easier and faster to use. It is true that APS and other physics journals like LaTeX format but if you look at other journals such as Wiley (Advanced Materials) and Nature, they prefer Word. In fact many journals want you to type in a pre-formatted word document that automatically takes care of the fonts, margins, two-column format, and image size.


Quote:
Originally Posted by switon View Post
Hi,

As I discussed in my earlier post, I recommended that the OP should learn to use whatever tools are required for the journal publications in his/her field: those might be Word, those might be TeX.

Next I'd like to address the comments that there are markups "all over the place" in LaTeX. In my experience, the only place in LaTeX documents that there are markups "all over the place" is when writing mathematics. For writing paragraphs without mathematics, LaTeX looks just like plain text. And, in my experience, the markups for math are no harder than manually writing the math symbols in the first place, such as writing \int_0^\infty for the integral from 0 to infinity. The nice thing about TeX is that this simple markup will correctly place the math symbols in the output whether the integral is "inline" in a text paragraph or whether it is in a separate equation line (the placement is different, by the way). Correct me if I am wrong, but I suspect that for Word you would have to specify two different integrals, one for the inline text and one for the equation line. Is this not true? So, when writing mathematics in TeX, the author does not need to be concerned with the formatting of the output, he or she can rather concentrate on the content, with TeX taking care of the proper formatting for you.

A comment was also raised about margins, implying that LaTeX had no way of setting margins easily; well, in LaTeX, you just change a single number and you change the margin spacing for the entire document. Isn't this also true in Word, don't you just change the margins for the entire document in a single spot? In LaTeX, if you change the page margins by changing that single number, then any "offsets" will also change appropriately, say those offset equations or highlighted boxes or figure wraparound paragraphs will all be automatically adjusted for you after a single margin change.

Let me ask about Word's equations? Benwiggy in his post states that "equations can be pasted directly in [ed. to Pages] from Apple's Grapher application". But do you know how hard it is to have to constantly have to paste equations into a document in the proper places? If you edit the equations, then you have to generate new images are repaste them? If you edit the text then you may also have to reedit and repaste some of the equations because now the old ones don't quite fit correctly. Pasting separate images for each equation in a physics or mathematics article is extremely time-consuming in my experience. How does Word handle equations?

Benwiggy also states that Pages handles the pasting of images, such as EPS and PDF, quite well and implies that it does so better than Word --- well, TeX was designed from the very outset (before LaTeX and PDF) to use Postscript and so it handles EPS and PDF with aplomb. Changing the size of an image requires changing a single number -- why you can even scale all of the images in a LaTeX document by changing one number: you don't have to individually scale each image.

I think there are important reasons why arXiv.org (physics), the American Physical Society, the American Chemical Society, and the American Mathematical Society request that all submissions be in LaTeX. Many individual journals also request LaTeX.

Now I have stated my opinions and backed them up with examples and explanations.

Personally, I don't like being called a "fanboy" without cause nor do I like having someone state "there's no way in Hell I would use something like LaTex" without backing up those statements with a reasoned argument. Maybe in your field you don't need LaTeX, and that is a perfectly good reason not to ever use it. But I don't think that you should then state or imply that LaTeX is worthless, especially when for some tasks there is no replacement for it. And many, many journals request submissions in LaTeX. If you don't believe me, go to the APS's or AMS's web sites and check their instructions for authors.

Respectfully,
Switon
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Old Jan 10, 2013, 07:36 AM   #45
switon
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RE: inline math, TeX, and web-based submissions...

(too long of post...removed)

Last edited by switon; Jan 11, 2013 at 08:29 PM. Reason: Added P.S.
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Old Jan 10, 2013, 09:49 AM   #46
switon
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RE: Word equations question...

Quote:
Originally Posted by vistadude View Post
Also for equations, word doesn't handle equations as images, they are pasted as standard characters, so they are always easy to modify when copying and pasting.
Thanks for the information...(removed irrelevant details...)

Last edited by switon; Jan 11, 2013 at 08:28 PM.
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Old Jan 10, 2013, 08:55 PM   #47
vistadude
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Switon, I had to use a dictionary to understand some of your writing. Are you a physicist or english teacher?

I now understand your inline equations, after reading it a few times. Indeed word is not great at complex equations. I never though about doing this and initially thought word could not do this. However, I just tried it now and Word does it fine. See below. To be honest, for most equations I use mathematica since it's easy to type equations fast without needing a mouse.

As for PDF, there's no standard for a pdf editor. Some people use adobe pdf or preview, but as far as I know, you can only put comments in the margins and you can't delete or cross out text and write over it. I might be wrong about this but that's what I see when I email pdfs to people for review, or they send their comments as a seperate email/word doc. Whereas with word, you can type over someones text but still see their old text, and you can put comments in balloons on the side.

Yes, word changed from doc to docx in the mid 2000's, but most people I know use still use doc. As computers get older, people replace them all the time. Apple abandons their software even faster than microsoft does, so we're all used to upgrading OS's, computers, and software. But we're talking about a graduate student. Surely he or she has access to a computer that's less than 5 years old and likely has word already installed.

As for your old version of word, you were using the equation editor, which was in it's own window. They have gotten rid of that since word 2007, and it's far more integrated. Additionally, equation editor was an optional tool, not everyone installed it (by default it is not installed). However, all recent versions of word install it by default, so you never have missing symbols when opening up a colleagues word document. Word has gotten considerably better, in fact I can't remember a time it crashed ( a couple times when it autosaves and you have many 10+ mb files, windows thinks it's crashing, because a save takes more than 20 seconds, but just let word do its thing).

I have no idea what you mean by ISO-8859-1, but it's a thesis. I'm pretty sure >95% of people don't worry about word and their thesis.

Btw, LaTeX users often save their documents as PDF to send to colleagues. Word users can do the same thing if they're worried about equations not showing up do to non-standard fonts or older versions of word.
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Old Jan 11, 2013, 07:53 AM   #48
switon
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Intercalated comments...

(removed extraordinarily long post that nobody would read...)

Last edited by switon; Jan 11, 2013 at 08:28 PM. Reason: Added P.P.S.
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Old Jan 11, 2013, 09:45 AM   #49
switon
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RE: English...impressions....

Vistadude, I'll take your remark as a compliment, albeit you may not have meant it as such.

(removed irrelevant personal details...)

"Impressions first, substance later." -- Switon, 2013 (and yes, you can quote me)

Regards,
Switon

Last edited by switon; Jan 11, 2013 at 08:27 PM. Reason: removal of personal info...
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Old Jan 11, 2013, 06:10 PM   #50
vistadude
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Hi Switon,

For the inline equation, I purposely used an extreme example with a double superscript limit, and I added an additional space too, that's why it looks weird. The spacing issue is not a word problem, it's just too much text without using spacing between lines, which is easily correctable. Btw, I don't understand what you mean by templates. Basically, you press insert, equation, and it adds a box for you to type the equation directly into the line of text. It's not the old days of word where it opens up a popup or subprogram. You don't have to worry about fonts anymore.

Yes, there is a way to output the source of mathematica, and you're probably right, it's Tex. I tried to look into this today, but it turns out my version of mathematica expired, and even though I don't have to pay at work for the new version, i'm getting tried of installing a new version which expires every 6 months. I think i'm done with mathematica.

I haven't tried Skim before, but I will download it. I actually use word for windows about 95% of the time only just because i'm faster with it from years of use, maybe there's a similar program to skim for windows.

I don't know if word can handle a huge amount of equations. I have seen professors write book chapters in word so i would tend to think it can. Plus word 2007 and newer is many times better than the older versions in terms of stability. But as you mentioned before, equation writing is slow in word because not many symbols have keyboard shortcuts like they do in mathematica.

I don't know if word can handle changing iso's. I've only tried the basic greek symbols like alpha, beta, etc and a few things like integral symbols. I'm going to guess it does not do this well.

The dictionary thing is a complement btw.

I think we've nailed all the major pros and cons of Tex and word. To each his own.

Cheers.
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