Software to write Scientific Papers

[brentd49]

I know there has to be a program better than Microsoft Word. When I try to move images/graphs around in MS Word they jump around all over the place. I end up having to reformat a paper 20 times because everytime I add a image, it effects the whole paper.

Or if MS Word is popular how do you control it from being random. I tried including tables, but to no avail.

What do scientist and engineers use to write papers and how do they include mathematical symbols into their papers? Is latex the most popular for script writing?

I was surprised google didn't give me an answer. So I'm counting on you guys to relieve my headache.

 

[Pengwuino]

MathType allows you to put formulas into Word documents. Also, you can make images separate from the text so that whatever you do to the picture's size or position, it won't effect the typing. I really forget how to do it though unfortunately... but it has something to do with putting a picture "behind" the text.

 

[primal schemer]

Most people I know (including myself) use LaTeX, it really is a great way to write papers.
Basically it takes away all of the formatting and does it for you, so you won't ever have to move images or tables around.

The only minor quibbles I have is that it can be awkward at first to put tables in (but once you've done it once or twice its ok), and pictures have to be in .eps format (or at least I havn't figured out a way to put jpegs etc. in)

It may take a couple of days to get used too, but it's well worth it.

PS

 

[ComputerGeek]

MathType allows you to put formulas into Word documents. Also, you can make images separate from the text so that whatever you do to the picture's size or position, it won't effect the typing. I really forget how to do it though unfortunately... but it has something to do with putting a picture "behind" the text.

you make a text box and then insert the picture in the text box and then turn the text box into a frame.

LaTeX is much nicer to work with however.

 

[ComputerGeek]

Most people I know (including myself) use LaTeX, it really is a great way to write papers.
Basically it takes away all of the formatting and does it for you, so you won't ever have to move images or tables around.

The only minor quibbles I have is that it can be awkward at first to put tables in (but once you've done it once or twice its ok), and pictures have to be in .eps format (or at least I havn't figured out a way to put jpegs etc. in)

It may take a couple of days to get used too, but it's well worth it.

PS

the graphix package allows you to use png (which is what I use)

 

[masudr]

I don't like reading papers not written in LaTeX. If you're a windows user then use MiKTeX if GNU/Linux (or some other UNIX variety) you've probably already got the necessary packages.

 

[Pengwuino]

How do you use Latex to make entire reports however. I thought it was only good for writing equations.

 

[dduardo]

You use styles and classes for the the look of the entire report. If your publishing in magazines like ACM or IEEE they actually provide these files on their webpage.

This is the program I use: http://www.lyx.org/

 

[-Job-]

The latest (free) OpenOffice release has an awesome math tool. I tried it, really simple to use and really cool.
You can find out more about it here:
http://www.openoffice.org/product/math.html

 

[ComputerGeek]

How do you use Latex to make entire reports however. I thought it was only good for writing equations.

LaTeX is a typesetting macro language for the TeX typesetting language.

it is used for equations because it is so good at it, but you can use it for anything you like, from Slides to resumes to reports (something it is very good at using its citation tools)

 

[franznietzsche]

LaTeX is by far the best. Don't use MS Word for these sorts of things. For starters, you can't even save directly to pdf. LaTeX is much easier to use, just harder to learn. Especially if you have documents with more than a trivial number of equations, figures with captions, etc. Things like writing in columns are automatically take care of if you specify colums. Images can be rotated easily, footnotes are much simpler. But it is somewhat difficult to learn.

Images to not necesarily have to be in eps. Normal ps works fine sometimes (in the windows world these may seem like weird image files to use, but they're really the most logical on other systems(well they would be on windows too, but nothing is done logically there), since you can just print any image to a file instead of a printer, which creates a .ps file, and you can then convert that to eps if necessary. The single standard makes life simpler.

 

[graphic7]

LaTeX is also the most portable solution. I haven't seen too many platforms that don't have a LaTeX port of some kind -- even something obscure like Plan 9 has one. So, if you want to learn something that you can take and use on any platform, LaTeX is the way to go.

 

[ZapperZ]

I know there has to be a program better than Microsoft Word. When I try to move images/graphs around in MS Word they jump around all over the place. I end up having to reformat a paper 20 times because everytime I add a image, it effects the whole paper.
Or if MS Word is popular how do you control it from being random. I tried including tables, but to no avail.
What do scientist and engineers use to write papers and how do they include mathematical symbols into their papers? Is latex the most popular for script writing?
I was surprised google didn't give me an answer. So I'm counting on you guys to relieve my headache.

Keep in mind that what scientists write for their manuscript may not be the same typeset document that you get when it is finally published. The publishers will do their own typesetting and have their own requirements on the format of the submitted manuscript.

Physical Review journals, for example accept Word and LaTex documents. They have templates for Word, and their own style document for LaTex (RevTex) that one can download from their websites. These templates are meant as a guide for the authors to judge the length of their papers (something one may need to know the publication cost, and for PRL since there's a page number limit).

In any case, typically, figures and tables are usually grouped at the very end of the manuscript, not inserted into the document (the editors will do this themselves). Mathematical equations are typeset in LaTex, or if one uses Word, using Equation Editor. Just don't be confused into thinking that what you see in the final version of the published paper is what we submit.

Zz.

 

[Moonbear]

Keep in mind that what scientists write for their manuscript may not be the same typeset document that you get when it is finally published. The publishers will do their own typesetting and have their own requirements on the format of the submitted manuscript.
Physical Review journals, for example accept Word and LaTex documents. They have templates for Word, and their own style document for LaTex (RevTex) that one can download from their websites. These templates are meant as a guide for the authors to judge the length of their papers (something one may need to know the publication cost, and for PRL since there's a page number limit).
In any case, typically, figures and tables are usually grouped at the very end of the manuscript, not inserted into the document (the editors will do this themselves). Mathematical equations are typeset in LaTex, or if one uses Word, using Equation Editor. Just don't be confused into thinking that what you see in the final version of the published paper is what we submit.
Zz.

I was starting to wonder if physicists had to jump through hoops that biologists don't! I write all my manuscripts in Word. Most of the journals I submit to have a PDF converter right on their submission website, so I just upload the Word document, and they do the conversion to PDF for review. Figures are usually done in a separate software; in my case, often PhotoShop or Excel, depending on whether it's an image or graph, and saved as a format compatible with the publisher's website again. Read the instructions to authors! A manuscript is formatted very differently from the final published version to make the review/editing process easier (such as double spacing and including line numbers).

I do know what you're talking about with trying to embed figures within a Word document though. When I prepare grant proposals, I need to do that to show the preliminary data, and Word can be really picky sometimes. I find it's easiest to just stick all the figures at the end and then move them to the right location after everything else is typed. When you insert the pictures, you have to go into the advanced options to adjust the placement, text wrapping, overlap, etc., or else it will really screw up your formatting if left to the default settings.

 

[exequor]

Most people I know (including myself) use LaTeX, it really is a great way to write papers.
Basically it takes away all of the formatting and does it for you, so you won't ever have to move images or tables around.

The only minor quibbles I have is that it can be awkward at first to put tables in (but once you've done it once or twice its ok), and pictures have to be in .eps format (or at least I havn't figured out a way to put jpegs etc. in)

It may take a couple of days to get used too, but it's well worth it.

PS

if you do a:
\usepackage[pdftex]{graphicx}

then something like:
\includegraphics{sample.png}
...would allow you to include jpeg, png, etc. I don't think that .gif works though.

 

[ZapperZ]

I was starting to wonder if physicists had to jump through hoops that biologists don't!

How do you think I keep myself this limber?

:)

Since I submit most of my work to the Physical Review family of journals, they're the ones I'm most familiar with. So I tend to use them as the prime examples since they publish the largest number of physics articles per month of any physics organization in the world. Their format calls for figures only in PS or EPS format submitted as separate files for each figures, whereas the text documents should be in LaTex (prefered) or Word. When you do this, you get a discount in the publication charges.

The editors typically reformat these and send the pdf files to the reviwers. These are further typeset when accepted into the familiar double-columned Phys. Rev. (or Phys. Rev. Lett.) format.

So software-wise, one has a lot of freedom to use whatever one wishes to do the figures, as long as they are finally saved as EPS or PS format.

Zz.

 

[robphy]

I was starting to wonder if physicists had to jump through hoops that biologists don't! I write all my manuscripts in Word. Most of the journals I submit to have a PDF converter right on their submission website, so I just upload the Word document, and they do the conversion to PDF for review. Figures are usually done in a separate software; in my case, often PhotoShop or Excel, depending on whether it's an image or graph, and saved as a format compatible with the publisher's website again.

Word, Photoshop, Excel... are not free. Word and Excel files are generally binary, as opposed to text-based (which is more easily archived and searched for its scientific content)... not to mention that nasty macros, virii, and possibly unintentionally hidden data might lurk within them.

LaTeX, as has been mentioned, is freely available on numerous platforms and operating systems.

Some related reading:
http://arxiv.org/help/submit#text
and
http://arxiv.org/help/faq/whytex

 

[-Job-]

I'd like to reiterate that OpenOffice (www.openoffice.org) has a math tool that does this. It's completely free (the whole package) and quite cool, give it a try, i thought it was nice, the interface is nice too, which IMO is more productive and easy to use than a markup.

 

[Moonbear]

Word, Photoshop, Excel... are not free. Word and Excel files are generally binary, as opposed to text-based (which is more easily archived and searched for its scientific content)... not to mention that nasty macros, virii, and possibly unintentionally hidden data might lurk within them.
LaTeX, as has been mentioned, is freely available on numerous platforms and operating systems.
Some related reading:
http://arxiv.org/help/submit#text
and
http://arxiv.org/help/faq/whytex

Nobody in biology even knows what LaTex is (I only know about it from these forums). Everyone has Word and Excel...I've never heard of anyone who didn't have it. But if you use something else, then you just have to format it to PDF yourself to upload it (I usually do that anyway because it saves some time during the upload). Some journals have begun to allow PowerPoint files for figures too, but I think that was a bad move on their part. They end up having problems with losing resolution, the conversion to PDF doesn't always work right, and then the publisher ends up needing the figures in some other format for actual printing because PowerPoint files are RGB, not CMYK colors. If you're doing research and submitting papers, it would be a pretty lame argument that you can't submit it because you have to pay for your software. That would be like saying you need to be able to submit hardcopies because you don't want to pay for the data jack in the lab to connect to the internet; it's just an operating expense you pay to do the work you need to do. But nothing we do requires publishing pages of equations. For that, it makes sense that physics and math journals would have a different standard. It's never that hard to find a computer somewhere at a university running whatever software you need to prepare a manuscript if a journal requests something different from what you usually use. For example, sometimes you want to create a graph that isn't a style found on Excel, so you ask around for someone using SigmaPlot and use their computer to generate that figure if you don't feel like buying it for just the one graph you need.

Bottom line is read the instructions to authors and use whatever the journal you're submitting to says you need to use.

 

[robphy]

Nobody in biology even knows what LaTex is (I only know about it from these forums).

Here are some: http://arxiv.org/archive/q-bio

If you're doing research and submitting papers, it would be a pretty lame argument that you can't submit it because you have to pay for your software.

...that is pay Microsoft and Adobe for software. (There is also WordPerfect and, yes, OpenOffice.) Apart from the cost of software, which is probably less of a problem here in US institutions, the more important point I was trying to make is the universality of text for portability and archiving. From http://arxiv.org/help/submit#text

Our goal is to store papers in formats which are highly portable and stable over time. Currently, the best choice is TeX/LaTeX, because this open format does not hide information. Note that for this and other reasons we will not accept dvi, PS, or PDF created from TeX/LaTeX source. Users of word processors such as Microsoft Word should save their documents as PDF and submit that. Note also that we will not accept scanned documents, regardless of format.

Some interesting lines from http://en.wikipedia.org/wiki/Microsoft_Word

Microsoft Word is the dominant word processor in current use, making Word's proprietary document file format (DOC) the de facto standard which competing products must support to interoperate in an office environment. File import and export filters exist for many word processors such as AbiWord or OpenOffice.org (see the article on word processor for other competitors). Most of this interoperability is achieved through reverse engineering since documentation of the file format, while available to partners, is not openly available. The document formats of the various versions of Word change in subtle and not so subtle ways; formatting created in newer versions does not always survive when viewed in older versions of the program, nearly always because that capability does not exist in the previous version. The DOC format of Word 97 was publicly documented by Microsoft, but later versions have been kept private, available only to partners, governments and institutions. Industry rumors claim some aspects of the Word file format are at present not fully understood even by Microsoft themselves. Lately Microsoft has stated that they will move towards an XML-based file format for their office applications.

Bottom line is read the instructions to authors and use whatever the journal you're submitting to says you need to use.

Agreed...

 

[franznietzsche]

Nobody in biology even knows what LaTex is (I only know about it from these forums). Everyone has Word and Excel...I've never heard of anyone who didn't have it. But if you use something else, then you just have to format it to PDF yourself to upload it (I usually do that anyway because it saves some time during the upload). Some journals have begun to allow PowerPoint files for figures too, but I think that was a bad move on their part. They end up having problems with losing resolution, the conversion to PDF doesn't always work right, and then the publisher ends up needing the figures in some other format for actual printing because PowerPoint files are RGB, not CMYK colors. If you're doing research and submitting papers, it would be a pretty lame argument that you can't submit it because you have to pay for your software. That would be like saying you need to be able to submit hardcopies because you don't want to pay for the data jack in the lab to connect to the internet; it's just an operating expense you pay to do the work you need to do. But nothing we do requires publishing pages of equations. For that, it makes sense that physics and math journals would have a different standard. It's never that hard to find a computer somewhere at a university running whatever software you need to prepare a manuscript if a journal requests something different from what you usually use. For example, sometimes you want to create a graph that isn't a style found on Excel, so you ask around for someone using SigmaPlot and use their computer to generate that figure if you don't feel like buying it for just the one graph you need.
Bottom line is read the instructions to authors and use whatever the journal you're submitting to says you need to use.

The problem isn't paying for Word, its the ridiculous limitations on the file format.

As robphy pointed out, text is a better solution all around for archiving purposes. LaTeX is easier to use, both for inserting figures, handling equations, graphs, general formatting. Its all easier in LaTeX. Its just harder to learn. Plus, LaTeX produced documents look better. Like an earlier poster, I dislike reading papers not produced in LaTeX, they just don't look right.

 

[ComputerGeek]

I'd like to reiterate that OpenOffice (www.openoffice.org) has a math tool that does this. It's completely free (the whole package) and quite cool, give it a try, i thought it was nice, the interface is nice too, which IMO is more productive and easy to use than a markup.

any tool that has you change focus from what you are typing is NOT more productive than markup like LaTeX.

it takes you about 2 -4 days to get a working understanding and you can then just type away.

 

[-Job-]

any tool that has you change focus from what you are typing is NOT more productive than markup like LaTeX.
it takes you about 2 -4 days to get a working understanding and you can then just type away.

Searching for how-tos on Latex, unless you have the whole markup on the tip of your tongue is not better either, it depends on how confortable you are with the language. Besides this tool allows you to write formulas with a markup as well (i don't think it's the same as LaTex though).

 

[robphy]

Searching for how-tos on Latex, unless you have the whole markup on the tip of your tongue is not better either, it depends on how confortable you are with the language. Besides this tool allows you to write formulas with a markup as well (i don't think it's the same as LaTex though).

How-tos on $$\LaTeX$$ are not that different from having a user's manual to Word or OpenOffice or any other software package.

http://www.openoffice.org/product/pix/math-big.png looks rather $$\TeX$$-like:
[ t e x ]\frac{G M_e M_8}{r^2}=M_8 \omega^2 r [ / t e x ]
$$\frac{G M_e M_8}{r^2}=M_8 \omega^2 r$$
compared to
[OpenOffice] {G M_e M_8} over {r^2}=M_8 %omega^2 r [/OpenOffice]

If the issue is the GUI-menu, there's this freeware tool http://www.dessci.com/en/products/texaide/ from the makers of the Microsoft Office Equation Editor [which, by the way, is not part of the default installation].
As mentioned before, there is Lyx's GUI http://www.lyx.org/LGT/math.php .
There's a handful of other such GUI-based tools.

(This discussion reminds of an earlier discussion on HTML publishing via a text-editor or via something like FrontPage or Word.)

Note that Maple and Mathematica can output in $$\LaTeX$$ (as opposed to OOMath). This implies the more universal acceptance of $$\TeX$$ for [mathematically-oriented] scientific publishing. It seems to me that the only thing that may compete with $$\TeX$$ someday is MathML or some variant of it.

my $0.02

 

[franznietzsche]

LaTeX is the standard for published papers. It is much easier to use. Yeah its hard to learn, no doubt about that. But once you know it, you don't even need a monitor to type up a paper. You just keep typing. I've typed out 10+ pages without having to touch a mouse to click on any thing. Its just faster and easier that way. Harder to learn, but much easier to use

 

[-Job-]

You must be pretty confident in your typing abilities to type without a monitor.

 

[ComputerGeek]

Searching for how-tos on Latex, unless you have the whole markup on the tip of your tongue is not better either, it depends on how confortable you are with the language. Besides this tool allows you to write formulas with a markup as well (i don't think it's the same as LaTex though).

you do not include learning curve when you judge productivity.

Once you get how to type equations, the text part is easy.. just type it.

you just need to know how to do what you need to get done. I guarantee that I could write a 10 page paper that has lots of in-line formulae and equations and tables in about half the time that you could using anything else. What I would like is for O to have an escape sequence to indicate a math mode and I could mark up an equation right in the document and have it render it when I save the file. That would give you the false sense of control and productivity you have in a WP but not make mathematical expressions so damn annoying.

 

[ComputerGeek]

the only thing that may compete with $$\TeX$$ someday is MathML or some variant of it.

my $0.02

EWWWW.. MathML is disgusting. nesting is NOT good for mathematical expressions.

 

[z-component]

EWWWW.. MathML is disgusting. nesting is NOT good for mathematical expressions.

I'll second that-- MathML is an ugly creation. LaTeX is worth learning if you want a professional look.

 

[franznietzsche]

You must be pretty confident in your typing abilities to type without a monitor.

Its not that hard to tell when you make a typo, if you spend a lot of time typing, typos will generally feel wrong. The hard part is knowing exactly how to correct it. However, the point is, using latex is that easy, once you know how. You just type. And then you're done. And it looks better than anything produced in a word processor that I've ever seen.