Submitting a Springerlink/Elsvier Journal Using LaTeX and Editorial Manager
So I ran into various issues this morning in trying to submit a journal to the Springerlink journal, Fire Technology.
As recommended by the journal, I was trying to submit my paper in LaTeX form. After all, I spent the time learning it for my thesis, might as well write the paper in it as well right? Yeah, especially as the Word template they provide is terrible and is a complete pain in the ass to use on a Mac (or a newer version of Office than it was designed for – so probably anything after 2003 by looks!)
Anyhow, the issues arose come submission time. The LaTeX title page was submitted fine and the LaTeX blind manuscript got uploaded along with the .bibtex file for the paper. They built the PDF and I noticed the references weren’t there but approved it anyhow – after all, they wanted bibtex files (it makes it clear in the preferences in the template TeX file).
Rejection
As you might have guessed, the file got rejected before the end of the day – I was kindly asked to add the references.
As much as I tried, the document would not accept the Bibtex file I was uploading, so I resorted to internet searching. Yet Google and DuckDuckGo couldn’t really offer a solution (though a few decent submission tips appeared such as this site) That was until I came across the American Society of Civil Engineers guide to Editorial Manager submissions (used by both Springerlink and Elsevier) here. Tip 1 and Tip 3 make clear that you should be uploading the .bbl file, not the .bib file. Now why don’t Editorial Manager make this clear? And if they don’t why don’t the journals?!
Either way, an attempt to follow those guidelines failed as well. At this point I was pulling my hair out and potentially having to re-write all the bibtex entries as embedded LaTeX references. Which is pain with it all formatted nicely in Bibtex and not easily convert-able to embedded bibitems. Or so I thought.
Success!
So in desperation I opened the .bbl to see what it contained. Well, lo and behold, it’s a converted Bibtex database!
\bibitem{AssociationofBritishInsurers2009}
{Association of British Insurers}: {Tackling Fire: A Call For Action}.
\newblock Tech. rep., {Association of British Insurers} (2009)
\bibitem{BureauVeritas2011}
{Bureau Veritas}: {Assessing The Roles For Fire Sprinklers}.
\newblock Tech. rep., Business Sprinkler Alliance (2011)
It was then simply a case of copying and pasting the entire contents of the .bbl file into the bottom of the blind manuscript file and commenting out the bibtex entries.
Uploaded the file and lo and behold, it worked fine!
Conclusion
LaTeX is supposed to make it easier to focus less on the presentation and more on the content. Why then, cant the journals and Editorial Manager make it clearer how to upload LaTeX files? I know that LaTeX appears to be dying out (most of the grad students in my department are using Word and don’t want to learn LaTeX) but if they seem to push LaTeX, why not make it clearer to those using it how they want the paper uploaded?
Now my only concern now is the layout of the references – on one hand, the paper submission told me to use a certain bibliography style but compiling and using that style in my referencing meant that the referencing in the article used Surnames, not numbers as it wanted so I used a different Springerlink referencing link – this could prove to be a mistake as well as the references section appears to potentially be displaying more information that needed.
All I can do now is play the waiting game.
Anyhow, I hope this helps those trying to upload LaTeX documents to journals for peer review!
Scrivener - Writers Software
So I’ve been trying some new writing tools for the thesis. Possibly a bit late in the game now but I’m still writing other things for various reasons, for example the UKAPU
newsletter editor and I’ve written a few magazine articles for the UK weekly computer magazine Micro Mart and not to mention I’m still writing academic papers.
So when I learnt of Scrivener , I thought I best give it a go. This app promised to be a great tool for those serious about writing so I thought I’d jump in. I won’t cover it in detail, others have mentioned it in other reviews online, I’ll just cover why it’s no good to me.
Impressions
Well I thought it looked good. Until I started playing with it and then quickly realised that it’s severely limited in terms of academic writing.
To write in LaTeX you need to either write it in LaTeX in the editor (and it’s not a great editor for doing that with I can assure you) and export the whole think as a text document or use Multi Markdown and then get that converted to LaTeX. Neither of which are done nicely in Scrivener (it lacks syntax highlighting, code completion etc).
it’s final nail is a lack of referencing software – referencing previous work is a cornerstone of academic research so this oversight is horrendous. It can be got around if you want to export your document to RTF format and use something like Zotero to reference your work (Zotero allows you to insert a reference citation field and then you can scan the compiled RTF document to add the references in).
Lastly, a lack of working Table of Contents system and ability to set headers/footers etc mean that for me, it’s a nice piece of software that goes wide of the mark. Perhaps for novelists it’ll be fine but for academic research, a few glaring omissions make it impractical.
LaTeX to RTF
So for a while, I’ve been using LaTeX to write up my work but every now and then someone wants a copy of my work in Word so they can edit it or mark it up and they cant use a PDF editor. This means converting my PDF into a Word document or my LaTeX file into a RTF document.
The PDF route was probably the easiest as everything was nicely laid out already and set out as it should be and various services on the web manage to convert PDF’s relatively well to Word documents such as Zamzar
However, the LaTeX to RTF option is also a possibility using the linux2rtf program however, that seems to be awkward at the best of times and annoyingly problematic at times. And it won’t run on OS X Lion because of the lack of Rosetta support (unless you build it in Macports but that requires a full LaTeX install via Macports as well!)
it shouldn’t have come as a surprise that the answer was staring me in the face all this time. I’d blogged about Pandoc before here and it’s ability to turn Markdown into LaTeX code. Well, it does that and more. Turns out it can output to RTF as well (that’ll teach me to RTFM!) so a simple command of:
pandoc -s LaTeX.tex -o Output.rtf
gives me a very well formatted RTF document that matches the LaTeX document style pretty well.
For example, in the document in question, I was making use of the url package and the verbatim package quite regularly – Pandoc understands these and formatted them as described in the RTF! Excellent! I don’t know how well it would come with Tables, References and floats but that’s to try another day but considering it handled verbatim and url fine, I have high hopes. latex2rtf is dead, long live LaTeX to RTF!
So once again, top marks to Pandoc for it’s fantastic ability to read and convert documents!
Texpad - Revisited
I’ve reviewed Texpad once before here. I said it was a good, native, Mac LaTeX editor that had a lot going for it.
Well the version I reviewed was v1.0 and now it’s on v1.26 so I thought it was about time to review it again to see how it’s improved.
Improvements
The biggest one that the developers pushed was the code completion feature. This means it’ll complete any code that you start typing and will auto type the finish (for example, LaTeX codes are inserted as \begin{} and end with \end{} and Texpad will automatically create the \end command of whatever you inserted as the beginning command.)
Not only that, but if you’re using Bibtex for your referencing and have already added the Bibtex file location to the file, Texpad will automatically search it for the reference as you type. For example, if the Bibtex key for the item I want is Salter2011, I can type \cite{S and Texpad will display a dropdown list showing all the names in the Bibtex file with Bibtex key that begins with S. This easily allows me to then find the reference I need without opening my Bibtex manager.
Open to All
Texpad, unlike some other text editors for the Mac, doesn’t allow for any font to be used in the editor. It’s list of fonts, whilst decent, doesn’t allow the use of personal fonts. However, after emailing the developers and asking if this could be enabled (so I could use the fantastic Mono Dyslexic font ), they sent me the following email.
Hi Chris,
Texpad 1.2.6 is in the AppStore now. Among other fixes and new features, there’s a hidden feature being delivered on your request, which I’m sure will be useful to many other users. Texpad now searches for installed fonts with the string ‘dyslexic’ in their name and lists them in the menu. I do not have the font you mentioned on my machine, but have tested the functionality with other fonts. I’d appreciate if you gave it a quick try at some point and let us know if Texpad correctly lists the fonts you need in the menu.
Merry xmas.
Jawad
And indeed, Jawad is right. The changes appear perfectly.
As can be seen, the font list shows the font and selecting it works perfectly. So the editor is now in a much better position to allow anyone and everyone access to LaTeX.
Overall
Overall the improvements have added to Texpad immensely. It’s now a very functional LaTeX editor that is constantly being updated and works perfectly well, with an active development team that are rapidly adding features and improvements to the software. Hopefully, 2012 will see the software improve considerably on it’s already fantastic base.
Texpad can be found on the Mac App Store .
Texpad - A Mac LaTeX Editor
I’ve written before on part of my thesis writing workflow here. I was testing out Mou, Pandoc and LaTeX and whilst it’s good for getting ideas down into cyberspace, it begins to fall down when you start introducing more complex LaTeX code into the documents. For example in my thesis, I’m using acronyms so I’m using the acronyms package and I also need to reference scientific data (as you’d expect!). But what editor to use on my Mac?
Past
In the past, I used to use the cross platform Texmaker 
but after using the Mac for a while, I found it ugly (ok, so that’s not a huge reason to hate it) and cluttered and I was looking for alternatives that fitted in more nicely with the Mac theme.
That’s when I found Texpad and decided to give it a try (it’s a paid for app on the Mac App store but there is a free demo on the Texpad website). It seemed to fit the bill but in what way and how?
Basically, when looking for a TeX editor, I want the following:–
- Syntax highlighting – hugely important to me so I can see the difference between text and commands
- Easy to see log output – should something go wrong with the LaTeX typesetting, I want to know about it and how to fix it.
- Commands – Easy to inset custom commands (though not as important now I’ve found Codebox .
- Navigation – allow me to jump to any point on the document where there are headers so I can start typing in the right section.
Texpad Interface
The Texpad interface fits nicely with the Mac OS X theme as it’s a native client. Plus points in it’s favour but not hugely important – however, it does support Lion’s full screen app feature and this makes it invaluable for long, distraction free writing sessions.
Plus Points
As you can see in the picture above, the interface is highlighted with the plus points – it’s a clean interface that allows you to input your work easily and with little fuss. The default display (if a PDF has been generated) is to display your code and the output PDF on the right. It’s a simple shortcut of ⌘+2, ⌘+3 or ⌘+4 to change between just the code, the view in the picture or just the PDF output (⌘+1 hides the navigation bar). Being able to easily view the output is a major plus point to me – Texmaker has it there but it’s not the Preview render view and so I often saw errors in the PDF output until I opened the PDF in Preview.
A major plus point I’ve found is that it hides all the temporary files such as the .aux files etc – these are stored in the same folder as the Tex file but in a folder called .textmp so are hidden by default in Finder – I like this as it keeps them there in case I need them but hides them from view as I don’t want to see them unless I have to.
Drawbacks
It’s main drawbacks are that it doesn’t support keyboard shortcuts for inserting code – by this I mean that ⌘+B does not insert the code for bold text like Texmaker does. However, in my mind, this is a fairly minor issue (⌘+B in this case runs Bibtex on the file). It’s other main drawback I can see is that it doesn’t follow the usual pattern of Mac applications and have ⌘+, open it’s preferences – instead the preferences are in the menu bar, however as there aren’t to many, this isn’t really an issue though does add some confusion. Finally, it doesn’t support Lion’s autosave feature. However, you can set it so that it autosaves on typeset which is what I have and I’m guilty of fairly often typesetting to see my changes so this saves it slightly though it might be a nice feature to bring in at a later date.
Conclusion
Overall, the cost is worth it for a native, good looking LaTeX editor that holds it’s own against it’s rivals. Try the demo out and see what you think. For me, it’s worth it as it fits my work flow in a nicer way than Texmaker does. However, I’d be interested to know what other solutions other people are using.
Markdown, Pandoc, Mou and LaTeX
For those that haven’t guessed already, Markdown is my new thing. It’s a fantastic little language that allows you to quickly write HTML and XHTML without knowing HTML!
Writing with it is quite natural (for those fans of Reddit, it’s the code method used to write replys) as it’s fairly simple.
# Item
gives a headline.
**item**
gives bold text etc etc.
After using it for a bit in Reddit, I found Mou , a Markdown editor for Mac that lets you type on one side of the window whilst in realtime, updating the HTML preview on the right. Simple, easy and elegant. I started using this for writing in Evernote . Write a note in Mou, which is simple, easy and quick (without worrying to much about the formatting) then copy and paste the right side into Evernote for an awesome looking note (at least it is until it syncs to the server – workaround is to export the HTML to a normal HTML, open in a browser and copy into Evernote from there – not so pretty and a bit long winded – have asked Evernote why it’s a problem)
In terms of quickly formatting a block of text, Markdown is pretty damn good. So much so, it got me thinking. Could it be used for academic writing? Turns out with another program, it can! Using pandoc , you can easily convert Markdown into LaTeX. The output is actually pretty impressive! Better than I have expected from cnversion software anyhow!
For example, we can take the help file from Mou as an example. It’s Markdown for a section is this . This corresponds to this in an HTML (what you see in a browser) which is this . Not to shabby. Load up pandoc and use the command
pandoc -s file.html -o file.tex
to convert the HTML file into a LaTeX file and you get the following LaTeX code . The -s flag means standalone and thus it adds the required preamble to the LaTeX document. This is then converted into PDF in the LaTeX editor (and with a few flaws, thanks to the .ico file type used by Mou in the help file which is unrecognised by LaTeX) you get this as the output.
As you can see, it’s a pretty good representation in LaTeX to the HTML file.
Conclusion
I use LaTeX to write my reports in – most, if not all get formatted and written in LaTeX using the new, but excellent, Texpad . This app is fantastic but remembering LaTeX commands can be a pain and it’s also slow at times when all you need to do is write down a draft. Once you start adding references etc, LaTeX starts to shine.
However, for the drafting process, using Markdown and Pandoc can speed up the crucial part of putting words on sheets and pandoc means that converting from Markdown to LaTeX will require as little possible time for the end user. Which can only be a good thing at the end of the day!
