Tag: latex

We’ve got tips

Writing the Thesis is a big deal, however right tools makes the experience a little bit easier..

I’m using Gedit on steroids, which is quite easy to achieve.

Just get the LaTeX plugin, and the to get all your files up and running in no time, try to gedit manager plugin.

Then use Classic thesis.

One more tip about screenshoots. Long story short, your video resolution will be always a bit short for the rendering in printing, so if you can’t use svg (made with Inkscape) or pdf or anything that is not a vectorial format you have to rescale (up) the png picture, which is tricky.. ’cause you’re trying to make more info from less.

However if you take the picture at top resolution you can use gimp scale tool to make a decent work.

To do that open the image (png, jpeg or what you’ve got) with gimp and then increase the resolution to 300×300 dpi and then change the canvas to a decent dimensions and scale it up.

This should make you rolling. Hopefully 🙂

Reviewing Paperpile 0.5 beta

paperpile logo

Paperpile is a nice software which hit the 0.5 beta version some days ago. It’s been a while that I’m using it and being in the full swing of writing my Thesis, I tend to use it on daily basis, so I decided to review it a bit.

First of all Paperpile is a reference manager, which help to manage, organize, cite and share the collection of scientific papers that you have on your computer. If you do science you know exactly what I’m talking about. If you don’t, imagine you have at least 200 different articles lying on your hard drive, which analyse different but related subjects. When writing a new research article, it’s necessary to cite all the relevant previous work to put you new work in contest. It’s the incremental delta of new information which science uses to evolve (when there is not a quantum leap).

Retrieving, organizing and citing those piece of work is necessary and can be a daunting task, but a good reference manager can help to make your life easier. There are several softwares out there, and I had different experiences, however it seems Paperpile is overcoming anything else and I’m using it productively, making me even to read more papers!

So let’s jump into it.

Paperpile general

General view of Paperpile

This is the general window of paperpile. On the Top left you can see the label la gmail. More than one label can be added to a paper and different background/foreground colour can be used to personalize it. To add an existing label to a paper just pick and drag it over it. Super easy.

On the Mid right you can add the RSS from journals, which can help you to be updated with the latest articles published. I used to have this RSS in my google reader, however having it directly in paperpile makes super easy to import new papers and collect the pdf.

Bottom right there is a collection of different tool, from being able to search Pubmed to import a directory full of PDF.

Central window is where the meat is. All the paper, ordered by addiction Date (you can change to what you prefer) and the most important feature: the search box. Paperpile implements a search as you type system, so as soon you start to type it it start to search in author title and also abstract.

One very interesting bit is that the search box actually find the article I’m usually looking for, and it’s pretty precise. It really saves me a lot of time. This is a clear edge over Mendeley for example, where the search was a disaster. At least in the version I’ve used so far.

The central window also give you the possibility to add notes to a paper.

On top left there are very useful actions which paperpile can perform for you. Paperpile makes easy to retrieve the article on to the publisher site, either giving you a link to visit the webpage or can automatically fetch the paper for you. Sweet!

Another very useful features, which I used so far at least 3 times, is the automatically generated email, which fire up an already ready to send email to your colleagues with the citation reference.

One last thing that I would like to put under the light is the LaTeX integration. With an easy Ctrl-K the label will be copied in your clipboard ready to be pasted in your LaTeX file. If you need the more standard citation, Ctrl-C will do.

To set up the automatically synch for your bibtex database just click on All Papers, on the top-left and turn it on, choosing the location for the file. After that every new paper you’ll add to your collection is automatically exported in BibTeX and you don’t have to care about it at all 🙂

Paperpile BiBTeX setting

Go and Check it out.

Best LaTeX editor: Gedit on steroids

Looking for a really powerful editor in GNOME is one of my constant research.

However it seems now it’s close to an end and it need just a small tilt to achieve perfection.
Right now I’m using Gedit with LaTeX plugin . It works amazingly and it does it jobs. The spellchecker is available and everything works properly.
I’m using Evince to actually check the complied PDF instead of the third panel, but that is a preference thing.

However the best tool out there to enjoy creative writing is definitely Scrivener. The main features of Scrivener is the ability to completely shiedl the user from the managing of the files and names, giving the possibility to focus on:

  • the status of it’s work (todo, draft, revision…)
  • the ability to shuffle and reorder the pieces of work as it best fit.
  • the main idea to use scrivener, or autonomous chunk of text which can be combined in an easy way

Writing books or big documents from scientific papers to PhD thesis it’s a main effort, which need constantly the main vision, but also the attention to details. Some parts will be ready before others, some pieces have a different evolution than others. The chunked text is the best way to go and I think it will really make the users’ life easier while battling with writing massive document.

The main problems with Scrivener are three according to me:

  • is available only for Mac and Windows, although there is a not supported version for Linux
  • the way the references are managed is not ok for scientific papers (BibTex does a perfect job)
  • not able to control easily the results of the compiled files.

This is the impression I’ve got when I used it for a really small period of testing. Although the User Interface is amazing.

Therefore we should create our own Scrivener, where the three points over stated should be addressed.

Gedit is a very good candidate to evolve, due to use of plugins, to a similar User Experience. Using the LaTeX plugin is already possible to holds and manage complicated text and notation and have a top-notch quality results.

What we are missing is the managing of the files a la Scrivener, where each file is a just a chunk of text which can be a subsection, a section up to even a chapter. Each file should be indexed and the metadata of each file should be tracked, like the revision status and the part status. A project manager, which will holds all this file and it will open them and make them always available to the user. The best would be to have a project manager which holds all the files, and a third panel where the status of the file and the type of the file is tracked properly.

Any chunk of test should be written in LaTeX and could be combined according of the order in the Outline, using the input command.

Unfortunaly I’m not too familiar with Gedit from the programming point of view, however if there is anyone who thinks is a good idea and want to give a try I’m happy to be a beta tester and give an hand.

If interested, leave a comment, or send me an email. There is a starting (hopefully) discussion also on the Gedit ML

Bibtex, some tips

I’m writing a report and I had to cite an article from a book. It’s one of this book which every article can also be used as a standalone paper. The problem is that if you use an article record, you will miss the book and if you use the book record, you will miss the article.

How to solve it? Google it! (somebody has already solved it and post it somewhere)

And it is. The solution is to use @incollection:

author = {John Doe},
title = {Dynamic Ambient Paradigms},
booktitle = {Paradigm Gems 2},
pages = {223--233},
publisher = {Addison Wesley},
year = 2005,
editor = {Averell Doe}

More BiBTeX tips (where I found this solution) on this page.

TiddlyWiki mandatory plugins

So if you are using tiddlywiki you know everything, if you don’t you maybe want to take a look to it.

What is tiddlywiki good for?

For me is good as an advanced lab book. Yes an electronic labbook. All my biology friends have a really good fashion old school labbook, but I’m not too much into paper and I keep forgetting things.

More over is really a pain to search on the paper… I have different thoughts and ideas that are completely disconnected and only at the end they make sense (sometimes…)

So here the User Case:

  • Able to write any piece of text/idea quickly in a not complicated way
  • Able to tag it in a flexible way and give it an automatic datestamp
  • Able to have this tool always available.

If you recognize this, you want to give a try.

Now I want to suggest you two plugins (I started to write this post because the second one was really hard to find again, so I will put the right link here. I don’t think google is going to care too much about this blog, but anyway it could help a bit)

First of the latex plugin (if you don’t know what is LaTeX … well I’m sorry..)

The second one is the listTaggedTiddlers

Give it a go.. It’s really cool.

The constant itchy: proper LaTeX GNOME editor

I have a constant itchy that I cannot get rid off: I want a smart and cool LaTeX editor for GNOME.

I would like to have something light and with a bunch of functions that could make my life easier.

Right now I use winefish which is doing a great job.

Strengths of this software:

  1. Integration with LaTeX tool and possibility to run them with shortcuts keys
  2. Wizard to introduce figures. Really useful
  3. Shortcuts to introduce LaTeX sections, LaTeX style and other stuff. I really love it
  4. Group project management. When you write with LaTeX seriuos stuff you have chapters… and I want to hit one button and get my document compiled. (E.g.: Three docs open: master.tex, chp1.tex, chp2.tex. I hit F2 and the program call pdflatex with master.tex as argument depsite which is my open document (i.e. chp2.tex.) This is one of the feature that I like most.

One big problem:

  1. Spellchecking is broken (LaTeX filter doesn’t really work)

It seems the way to go is enchant.

Now, winefish is written in C and it’s not really my cup of tea…

What I saw is that there is this pyenchant and the interesting bit is here

It seems there is going to be a support for the LaTeX filter soon (hopefully). This means that if there is an editor that is able to implement the pyenchant API we (if you read ’till here is also your problem…) have resolved our problem about an editor with a correct spell checking in LaTeX mode.

So looking around I stumbled to this scribes.
logo scribes

It seems to be under big development (infinite development?) but it seems the version 0.4 will implement the pyenchant.

Now I see two possible solutions here:

  1. Fix winefish. This means:
  • Port somehow the enchant library to winefish. It’s in C. No, it doesn’t sound easy. Winefish is a fork of an old version of winefish. Now the development has stopped ‘casue the main developer didn’t have anymore the time.
  1. Fix scribes: This means:
  • Test the development version. Check the spellcheck works. Contact the guy who is working on pyenchant and speed up the filtering process for LaTeX filter.
  • Implement the snippet feature to insert custom text in the document (doable.. there is this possibility)
  • Implement at least a wizard for the figures.
  • Check out the project management

So you’re thinking that I should go for scribes. I don’t htink so, the autosave function will kill me and there is no undo function.

So maybe you said that I should look to GEDIT again and think about the LaTeX plugin… ‘Cause GEDIT will use or is going to use enchant. I’ve tried. I didn’t like it. I use GEDIT to open every txt file whatever is the content. So it should be light and quick. I said light and quick. The plugin is getting my GEDIT really slow. MKore over the spellchecker it’s not working.. So what we are talking about?

I would like to fix my first love winefish.

Or maybe stick to reality. Use winefish and run

aspell -t -c file_to_check.tex

or even use Texmaker

The spellchecker works really well, but I’m missing my powerfull shortkeys that I have in winefish.

Or maybe I should write another bloody editor in the right way (TM). (I won’t to reinvent the wheel for the n+1 time. It’s stupid and it’s not the way to do it.)