Hi all

my apologies for not replying sooner than this. I have been trying to find out what it was that led to the strange problems and eych time I thought I knew what it was something else turned up (see under 3a below). Maybe I need to tell you what it is that I am trying to accomplish and start over.

The problem I am trying to solve is that in my field of science (molecular biology) MS Word is the de facto standard for exchanging manuscripts among collaborators and also submission of manuscripts to journals. I can't for the life of me tell why this is because frankly you couldn't agree on something less suitable for the job. <Argh> The things that are particularly annoying are the track changes feature because it does one thing well (point out small changes in an otherwise constant environment). This encourages people to muse over the choice of the right adjective when in reality the architecture of the paper should be discussed and altered. On top of this it makes Word really slow and unstable especially when Endnote is used in conjunction with it. I am sick of this because it is not what I need most - a working environment which lets me concentrate on finding the best way to present my research not struggling with the formatting. Finding the spots that have been altered by a collaborator, however, is a very real necessity it just should not get in the way.

Although this may sound as if I was trying to make the typical Latex case, this is out of the question for a number of reasons. The acceptance amongst students is too low, they all grew up without knowing what a command line is after all. Most journals accept manuscript only as Word documents, not RTF, PDF or Latex, so there shoudl be at least the option to export from whatever I chose to write in as a Word document.

that leaves me trying to solve several problems:

1) finding a writing environment that disregards formatting, is easy to learn and easy to read while writing. 2) Some kind of support for bibliography tools should be incorporated. No hidden field functions that only work (hmm, work...) in some versions of Word and screw up everything every now and then. Plain text, please. 3) a tool that would point out where changes have been made by others. By this I mean both sublte changes like insertion of a word or a paragraph somewhere, but also more complex changes such as a sentence or a paragraph that has been moved elsewhere. 4) all this would need to keep working (for me) even when collaborating with others who prefer other tools. I very rarely write all on my own, so a solution that would only work if everybody else would use the same tools would not improve anything.

My plan was as follows: 1) Multimarkdown seems to hold a lot of promise as it is easy to read and not complicated to learn. the support for math is limited but this is not a major requirement anyway for me.

2) bibliography tools such as Endnote, Bookends or Bibtex should work as they insert text placeholders that get scanned and turned into citations later on. The only thing I would loose is Cite-while-you-write (the instant formatting) and the traveling library. These two features I switch off right after installing Endnote, so no loss here.

3) That's a tough one. a) The simple changes (insertions, deletions) should be easy to keep track of. I say should because I found it to work very well as long I only used a dummy file that I saved and compared after doing some changes. However, when I took two revisions of a real manuscript that I saved as text files from Word, the result was much less enlightning. Both Filemerge as well as kdiff3 that worked well with the dummy files indicated huge areas that were changed according to them even though these included whole pages that were not changed. Why this is I don't know.

b) the more complex changes are sections of the text moved elsewhere. I am still on the lookout for the right tool for the job. If anyone knows a tool that would do that let me know, otherwise I'll write something myself.

4) Multimarkdown allows exporting RTF and .doc. I haven't decided whether Textmate or Scrivener which support different aspects of MMD would be easier to use in practice for the purpose.

My apologies for the long post. I would appreciate any and all helpful comments

Christoph

On Jan 20, 2007, at 12:14 PM, Christoph Prion wrote:

[...]

The problem I am trying to solve is that in my field of science (molecular biology) MS Word is the de facto standard for exchanging manuscripts among collaborators and also submission of manuscripts to journals.

[...]

1. finding a writing environment that disregards formatting, is easy

to learn and easy to read while writing. 2) Some kind of support for bibliography tools should be incorporated. No hidden field functions that only work (hmm, work...) in some versions of Word and screw up everything every now and then. Plain text, please.

[...]

My apologies for the long post. I would appreciate any and all helpful comments

Christoph

Hi Christoph,

don't worry about it. Your question may be off-topic but, I think, still interesting to others. At least, I have the same problem, which also means that I have no good solution for you. What I am currently doing is:

- Write my research proposals and other long documents that are supposed to look good in LaTeX, using Textmate/PDFView/BibDesk - Write my paper manuscripts in MS Word, using EndNote (library imported from BibDesk) - Write my notes and summaries of scientific papers (all things needed for future use in articles, reviews, proposals, or as introductions for new students) in RTF with basic formatting so that I can later reuse these either way (e.g., references in curly brackets so that EndNote will recognize them when I copy it to Word, and I only have to add \cite when I use it in LaTeX)

Pretty clumsy. And the more complex part of your problem (compare files) has been done manually by myself. The use of Markdown was new to me, and I only checked it out after you mentioned it in one of your last emails. It sure looks interesting.

I would also like to see some helpful comments on this issue.

Best regards Holger

Mark

ooops. For some reason am having a rough start here on this list because I never see the the mails I am posting myself turning up in my inbox. This is why I sent my very first message (ahem) about five times...I made doubly sure that "receive your own message from the list" was checked.

Sorry if you felt ignored after replying to that other thread. There are two kind of problems. First, diacritics (ä, ü, é) are not displayed corrrectly. This is probably solvable but I haven't investigated. Second type of problem I have outlined in my last post. In short, it is the fact that FileMerge (just like the other tools) becomes very generous about the size of the context in which changes exist between the files. Third (nobody expects the Spanish inquisition!) when dealing with large files, the trailing edge regions of the file FileMerge displays contain many errors and also parts that both documents have, are missing in FileMerge. I don't exactly know if this is triggered by the files being UTF-8 encoded. I happened to realize it first with UTF-8 files and this put me off enough to exclude FileMerge from further testing although I liked it visually very much.

On Wikipedia it is mentioned that Filemerge expects encoding Roman. I'd be glad to hear your comments on this and recommendations on how to solve the diacritics problem.

Thanks Christoph

On 1/16/07, Mark Eli Kalderon eli@markelikalderon.com wrote:

I use the FileMerge bundle. What problems are you experiencing with UTF-8? If it is a problem, there is a diff frontend wdiff that yields word differences. It can be found on Fink. It should be relatively easy to build a word difference bundle around it. All the best, Mark On 16 Jan 2007, at 09:59, Christoph Prion wrote:

...

Hello all I am new to Textmate and this list but so far really impressed by the program and the people posting here. My background is in molecular biology and I will mostly use TM for text (MultiMarkdown is appealing to me) not so much code.

Although I am slowly making my way through the manual I have not found anything that would allow me to compare two textfiles and highlight changes between them. "Diff" is not what I am loooking for because it is based on lines. Writing manuscripts I don't use carriage returns so a single difference in a paragraph will highlight the whole thing not just the difference only. FileMerge (in the Apple developer tools) is much closer and also visually intuitive, but getting long in the teeth and having difficulties with UTF-8.

Is there a Textmate bundle that will do this kind of comparison for me?

My sincere apologies if this question has been answered already,

Christoph

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