latex

Quick and easy posters in LateX

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Going to a conference and have to print a poster? Here is my tip for doing this as efficiently as possible.

Since my first conference, I have made quite a lot of posters (and printed them all on fabric) The first time this was very time-consuming, but the time I spend per poster has decreased over time. My new record is from the last conference. I had scheduled the task of creating the poster on my calendar – by default all events are one hour long. But by the end of the hour, I had not only made the poster, I had also already ordered it from my favorite vendor. All I had to do was wait for the poster to arrive.

As a disclaimer, I do not have the best posters, so if you want to win the best poster award, this is probably not the advice for you. But my posters do the job. So far my experience is that it’s more important how I talk about my research while I’m at the poster. That’s 20% of the work that achieves 80% of the result. The poster can fill up the 80% of work that achieves the other 20% – with all the other things we need to be doing (writing?) the decision on not spending too much time on it is not so difficult.

My “secret” is to use the same LaTeX template and the same structure for every poster. The template takes care of the layout and doesn’t let the poster get too crowded, and the structure guides me in what content I need to add.

I’m sharing two zip files with source files for my posters – one with a TU Delft, one with a TU Eindhoven template. When I was at Erasmus Medical Center, I could not find a LateX template, so I modified the TU Delft one to use different logos and colors. These templates were not originally made by me but allow modifying/sharing as long as the copyright notice is included. Please do the same if using the templates.

Cheplygina et al – Characterizing Multiple Instance Datasets (Poster, TU Delft template)
Cheplygina et al – Exploring Similarity of Medical Image Datasets (Poster, TU Eindhoven template)

Multiple Overleaf projects with a single .bib file

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I recently discovered that one of my biggest dreams – being able to link all my online LateX projects to a single .bib file (but without using Mendeley) – is possible!

Previously I had “solved” this problem with ShareLateX projects, by writing a script that copies my main .bib file to several project folders every hour. However, this requires Dropbox sync for ShareLateX, which is a premium feature for new users. Not to mention, it’s not ideal to do it every hour, and to have to update the script when you want the .bib file to be copied with an additional project.

Now a much simpler solution is possible with Overleaf. It’s probably been there for a long time, but I only realized this now. When you add a new file to an Overleaf project, there is an option “Upload from URL”. I thought this option would do just that – get the file from the URL and upload it. But what it actually does, is remotely link to the file. That’s the solution right there! (Thanks to Overleaf’s Dr. LianTze Lim for pointing this out!)

Here are the steps to get this to work:

1. Put your .bib file in Dropbox, set the sharing settings so that it’s accessible by anyone with the link. Copy the link

2. In your Overleaf project, Go to “Files”, then “Upload from URL” and paste the link here. With Dropbox, this link will end in “dl=0”. Change this to “dl=1”

If this works correctly, you should now see your .bib file in your project, but with a “linked” icon next to it

3. Proceed as you usually would with a bibliography file

If you are collaborating with others, the best way is probably to have two .bib files – the linked one (not writeable from Overleaf) and another one that is local to the project, for any new references. This way at the end of the project, you could move all the new references to your main .bib file.

I also tried to do this in ShareLatex, but couldn’t find this type of option. Although ShareLateX has free Dropbox sync because I’m an early user, this feature of Overleaf could have convinced me to switch (even if losing the sync). But Overleaf and ShareLateX are merging, so I’m hoping I might get to enjoy the benefits of both.

How I manage my bibliography with Evernote and Jabref

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Today I’m staying with the theme of managing bibliographies (see my previous post on syncing .bib files). Now I describe the process of how I actually add papers to my bibliography, and keep track of my bibliography with Evernote. This process is fairly recent so this post is rather an exercise in me thinking out all the steps, but perhaps it might be useful to somebody else.

Capture

Most of my ideas for which papers I should read come from Google Scholar Alerts or Twitter. When I think “this might be interesting”, I immediately save the PDF (if I can access it) or the link to my Evernote inbox.

Organize

As part of my weekly review, I go through all the notes in my Evernote inbox. When the note is a paper, I decide whether it’s really something I want to read, and if yes, I now definitely get the PDF and put it into the note. I also rename the note by its Bibtex key, for example “cheplygina2017transfer” for a recent paper of mine where the first word in the title is “transfer”. Then I tag the notes with different keywords, which tell me what topics the paper could be relevant for.

I then move the paper to either “Literature Inbox” or “NextPaper Inbox” notebooks, where NextPaper is the “codename” of the paper I’m going to submit next.

Process

OK, so now the papers are collecting in these two literature inboxes – what next? I need to actually read some papers. Recently I’ve been scheduling tasks like “Process 5 papers” on my calendar to get this done. When I do this I usually select papers which have similar tags, which I would write about in the same section of my paper.

Then I go through the paper and type notes in Evernote, in the same note that already has the PDF. This (the note writing) is inspired by Dr. Raul Pacheco-Vega’s “PDF to memo” method.

This should give me an idea of what I want to say about the paper, if I reference it later. I might also add or remove tags as needed. I can also add Evernote links to other related papers, although I don’t do this very often.

Once this is done, I move the note to “Literature Processed”. This is also when I get the bibliographic details of the paper (by searching the title on Google scholar), and add them to Jabref (by copying and pasting the .bib details). It is also possible to add a link to Jabref that will open the corresponding Evernote note, but unfortunately this uses the URL field, so you wouldn’t be able to have links to both Evernote and the online source of the paper.

Reference

I also schedule tasks like “Literature Processed to 0” which means I have to actually include the processed papers in the paper I’m writing. I go to the section where I want to reference the paper and write something about it, based on the notes I made before. This is also a good check to see if I really have the biliographic details – if I don’t, ShareLateX will not suggest me the reference.

Finally, I tag the note with “NextPaper” since that’s where I referenced it, and move it to the “Literature Reference” notebook. I should review these tags upon publication of the paper (I haven’t gotten to that part yet since I started using the system). But if the tag stays, I could even include a short snippet of what it is that I said about the paper.

Future projects

In a next project I might want to reference some of the same papers that are in Reference, and do not go through the process above. However, once I’m working on “NextPaper2”, I can just go to my Reference notebook, do a search for the relevant tags, and then tag those papers with “NextPaper2”.

Verdict

This is not a perfect system, since several things to be updated manually. Perhaps Mendeley or Zotero sort out these things for you – I’ve tried both in the past and was never quite satisfied, but this was before I had this process in place.

The process – not the tools – is probably what is helping me the most. But another advantage is that I’m using tools I already use a lot. Since I have Evernote open all the time, it’s easy to decide to read a paper, when I have a bit of time before my next meeting, for example. It also gives me a overview of how much reading/writing I need to do, based on the number of notes in each notebook, and it’s rewarding to see the “Inbox” numbers go down. I think I’ve got the ingredients to successful habit adoption right here – now hoping these will in fact translate to written AND published papers.

How to use a single .bib file with multiple ShareLateX projects

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I’ve been using ShareLateX, which lets you edit your .tex documents collaboratively online, for years now. I’m happy with it, except one thing: you have to have a different bibliography file per project. In this post I explain a workaround I created for this problem. It’s not beautiful and requires that you use Windows and have ShareLateX premium, but if you have a similar problem, read on!

A better workflow

If you are like me, you generally “manage” your bibliography by the following method:

  • Copy-paste .bib file from a recent project
  • Copy-paste new references from Google scholar while writing
  • Clean up all the missing fields etc, when paper is ready for submission
  • Forget you did this, and do this all over again for the next project

Sure, it’s possible to have a single master bibliography offline, and then every time you add a reference, to export the bibliography, and import it in your current projects. But this is a bit time-consuming, so I decided to find a way to automate the process a little bit. There are four steps to this:

  1. Create a clean master bibliography in Dropbox
  2. Enable syncing between ShareLateX and Dropbox
  3. Set up script to copy master bibliography to ShareLateX folders
  4. Schedule the script

Master bibliography with Jabref

The first step to a better system is to actually have a cleaned up bibliography file that you will WANT to use. I do this in Jabref, because it is as close to “just editing .bib files” as I can get, has everything I need, and is free/open source.

To finally create a single bibliography, I copy pasted the bibliographies from my MSc thesis, my PhD thesis and my papers since my PhD into a giant .bib file. This created lots of duplicates, but these can be edited in Jabref. This was quite neat, since it allowed to me to choose the “most cleaned up” version of the reference. This was a time-consuming process, but hopefully with this system I don’t have to go through it again. My master bibliography now lives in a Dropbox folder called “Bibtex”.

 

ShareLateX – Dropbox sync

The next thing that I needed is syncing between Dropbox and ShareLateX. Unfortunately this is a premium feature at this time.

If you have the syncing enabled, each paper lives in its own Dropbox folder, under Dropbox/Apps/ShareLatex. Here are mine:

Each of these folders has a .bib file. Although locally I could ensure that the projects link to my main bibliography file in Dropbox/Bibtex, I cannot do this in the cloud.  (Or, there is a way to do this but I haven’t found it, which would render this blog post obsolete).

 

Copy bibliography to project folders with a script

My “genius” solution is to copy my master bibliography to the individual project folders. Of course I don’t want to do this manually – I want an “if this then that” solution that does it for me when the bibliography is updated.

In the end I settled for a slightly simpler solution of “copy every hour between 8 and 17” (when I’m most likely to be writing). Not as elegant, but (at least in Windows) it’s the 20% of effort that gives me 80% of results.

To copy files automatically, I used a Powershell script that says what to copy and where, and the TaskScheduler, which actually runs the script.

The Powershell script is called jobBibtex.ps1 and has the following contents (you can just create it with Notepad, but be sure to save it as “other” and not as a text file):

[sourcecode language=”plain”]

$SourcePath = "C:\Users\Veronika\Dropbox\Bibtex\refs_main.bib"
$DestinationPath1 = "C:\Users\Veronika\Dropbox\Apps\ShareLaTeX\Crowd2018"
$DestinationPath2 = "C:\Users\Veronika\Dropbox\Apps\ShareLaTeX\Survey2018"

Copy-Item –Path $SourcePath –Destination $DestinationPath1 -Recurse
Copy-Item –Path $SourcePath –Destination $DestinationPath2 -Recurse

[/sourcecode]

The script now has hard-coded in it which projects it should copy to. A better version would go through all the folders in Dropbox/Apps/ShareLatex – this is the next improvement on my list.

Schedule the copying script

The last thing is to schedule the copying script. I used this tutorial to get this done, but here is a short summary. From the start menu, search for the TaskScheduler program. Once there, go to “Actions” and “Create basic task”

 

In the menu that comes up next, you need to select a name for your task (“Copy bibliograhy”) and select a trigger, for example “Daily at 8AM”. As the action, select “start a program”.

The program that you are starting is Powershell.exe, and you need to add the following argument (replace the path with wherever you saved your .ps1 script:

[sourcecode language=”plain”]

-ExecutionPolicy Bypass C:\Users\Veronika\Dropbox\Scripts\jobBibtex.ps1

[/sourcecode]

Save the task and run it to see if your .bib files were really copied!

80/20 rule

Clearly this is not a perfect solution.

  • This is a one-way sync, so editing a copied .bib file on ShareLateX will not reflect in your master bibliography. This is problematic for collaborative projects. My solution would be to have two .bib files in each project – one with the master bibliography, one with additional files your collaborators want to add (which you could later add to the master .bib file).
  • The projects which to copy to are now hard-coded in the script – it would be better if if the script would work for any new folders in Dropbox/Apps/ShareLateX
  • Copying every hour is too much, a “when updated” copy would be more neat

But, it is the 20% solution that gives me 80% of the results I wanted, and hopefully will save me time in the future.

 

Do you have similar solutions in place? Leave a comment below!

Firsts: Submitting and revising a journal paper

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This post contains the history of my first journal paper, “Multiple Instance Learning with Bag Dissimilarities” (also available via my Research page).  Recently I shared some examples of cover letters and responses to reviewers with people on Twitter, so I thought it would be informative to put it all together in one place, including a timeline of the process and take-home messages. Note that this is not a guide how to write a paper or how to respond to reviewers – but if you are looking for that Dr. Raul Pachego-Vega has lots of resources for this.

On with the story of the paper. The files (draft, original and revised submissions, cover letter, reviewer response) are all  here (.zip), but the post should be readable without them.

Draft to first submission

In my PhD years 1 and 2, I had a few workshop publications which were exploring different aspects of one idea, and it was time to put these results together into a journal paper. I made a first attempt to organize all my ideas in November 2012. This first draft then went through several iterations of discussions and comments with my supervisors. Finally, on the 25th of March 2013 I submitted to TPAMI. I think the plan might have actually been to submit to Pattern Recognition. But as I understood at the time, TPAMI was more impressive to have, and had a faster review process, so it was worth a shot.

When submitting, I did not consider anything else I would need other than the paper, like a cover letter! Therefore my cover letter was very short and uninformative. I only mentioned that the journal paper was based on earlier conference submissions, but not what the differences were. It seemed obvious to me that the journal paper was so different, that I didn’t need to explain this. Of course, after a few days I received an email (I remember having this stomach sinking feeling) that I needed to provide a summary of changes, which I did. It seemed my paper was still under submission – crisis averted!

Take-away: if the paper is based on any conference publications, explain the differences in the cover letter, even if you also do this in the paper

Rejection and another submission

The part about the fast review process was true. On the 5th of June 2013 I received the decision that the contribution was not significant enough for TPAMI. Since my paper wasn’t immediately rejected after submission and actually went to reviewers, I was quite satisfied with this result.

After updating the paper according to the useful comments I could extract from the reviews, on the 26th of June 2013 I submitted the paper to Pattern Recognition. Once again, the submission system caught me by surprise! While I now had a better cover letter, I now also needed to provide a “graphical abstract” and “highlights”.

Take-away: go through the submission system of the intended journal before you actually want to submit there. Another surprise I’ve encountered in other journals is that I could suggest names of reviewers – it is good to think about this beforehand, while you are writing the paper.

Major revision and responding to reviewers

As expected, the review process at Pattern Recognition was a bit slower. On the 23rd December 2013 I received a “reject and resubmit” or “major revision” decision. This was a more hopeful situation than with TPAMI, so I started revising the paper and writing my response.

A useful structure for the response is:

  • reviewer comment (in bold)
  • your response
  • quote from the updated paper which shows your changes (in a different text color)

Take-away: simplify the life of the reviewer, they likely do not exactly remember your paper and do not want to go through the whole thing, switching between the document and the updated paper, to see if their proposed changes have been made.

What I did wrong the first time around, is that I would do the suggested change in the paper and in the response, then would discuss both the paper and response with my supervisors. This was not productive – since they proposed changes to my change, I would have to modify two files!

Take-away: write the response first, include proposed changes in the response, then discuss with supervisors, then add changes to the paper!

Another annoying thing was that in my response I was referring to section numbers and references in the original paper. But since these would get updated (due to new sections or references), I would have to keep changing these by hand in the response. But, it turns out there are LateX packages for this too! See this answer on Stackexchange.

Besides the responses, we added a “cover letter” to the beginning of the response, explaining that we prepared a revision and summarizing the changes made. After a month or so, I submitted the revised paper! I was confused about filling in a “cover letter” text field in the submission system – after all, I now had a whole response to reviewers, that was a cover letter in itself. But I think I just copy pasted “cover letter” from the response, with a comment that detailed responses can be found in response.pdf.

Minor revision and accept!

Then finally, a long-awaited email came on the 20th of June 2014 – “We would be happy to publish your manuscript […] in the journal provided that it is revised in accordance with the enclosed referee comments.”

A minor revision! I remember exactly where I was at the moment – on a camping in Sweden, getting ready to celebrate midsummer. I was walking back from the bathroom to our tent and decided to check my email on my phone, and there it was. I’m pretty sure I jumped and yelled “yes”, or something of the sort. But it was great that I was already at a party, so I could celebrate this event immediately 🙂

Take-away: don’t forget to celebrate!

I sent in the revised version a few days later, and on 21st of July 2014, the paper was accepted, and in early 2015, published. A nice detail is that at the moment the paper was published, it already had a couple of citations – because I uploaded a preprint to arXiV back in 2013. See my blog post about this and a great post by Niko Kriegeskorte if you are still unsure.

Take-away: upload your papers to arXiV

Share your experience

Have you had a very long, or perhaps a very short review process? Surprises you encountered during the submission process? Or do you have any other tips about submitting papers you could share? Please leave a comment below!

Writing papers online with ShareLateX

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I’m working on a paper together with a PhD student who is technically in my lab, but geographically in Cuba. For some reason, neither SVN nor Dropbox were working, and I was afraid we would have to resort to emailing the paper to each other (the horror!). Then during lunch I thought that we could just use GoogleDocs for the LateX file, or maybe that GoogleDocs even supported LateX. It’s such a simple idea somebody had to already have thought about this!

And indeed, ShareLateX has! You can sign up and create LateX projects and invite others to collaborate with you. Then you have your main file, any other files you want to add, and a button that compiles the .tex file into .pdf (and you can even choose whether you want the latex or pdftex version).

Again, the idea might seem very simple, but I’m still somewhat in awe… You can work on the same LateX file real-time, without waiting for somebody to save, commit or upload a new version. This is very motivating because you see the paper changing so quickly. It is also much easier to decide things together, such as adding that new section, because you already see how it would change the paper. Last but not least, you are all using the same compiler, so you can’t mess up the tex file for each other 🙂

There is  a down side, of course. The free version only supports 2 collaborators and there is no version control. As soon as you want an upgrade, you get the “Collaborator” account which allows 10 collaborators per project but also costs you $15 a month. Not a lot if the only thing you do is write papers with people overseas, but too much if that only happens once or twice a year. I only hope that universities realize how service is great for the researchers’ productivity, and offer it to employees free of charge 🙂

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