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13
May
2011
Tools I use in my research -- part I

In Academia, usually there are classic softwares used, e.g., Microsoft Office, and in very extreme cases also Matlab and advanced plotting softwares such as Sigmaplot. I have nothing against using them, apart from they do not offer what I look for: (i) flexibility, (ii) extendibility and openness, (iii) fun/ease of use, (iv) power, and (v) price.

 

I constantly seek for new alternatives, and here I share with you what I use on daily basis. Hope it will help you a bit too. I have a MacBook Pro, and an Ubuntu linux server setup.

[Plotting] Veusz: This is an incredible nice piece of software, available for many platforms. I can do nearly whatever I want with Veusz. You can also use LaTeX strings in the plots. The output is a production-ready pdf (or other image types), than I automatically import to my writing setup. The data can be also automatically imported from your text files (cvs also). So, this is my normal routine:

I get the simulation results in a text column format. Veusz is automatically imports the data. I modify my model and get a new text date, and then hit the "refresh" and voilà! the new data are plotted.

And it is free!


[Document processor] Yes, there is office 2011, which looks quite good. But I use LyX, and love LaTeX. It has a learning curve (though with LyX it is quite low).

LyX is a document processor that encourages an approach to writing based on the structure of your documents (WYSIWYM) and not simply their appearance (WYSIWYG). 

[Source Control] Yes, I do use source control, and you should too. Git (and GitHub) is my choice of source control, as it is context based, in contrary to SVN. SVN  is also very nice and I used it for years.


[Data fitting] Matlab is a good choice for the classic problem of data fitting. There is now another class of these tools, which does not fit your data to a prescribe category of fitting algorithms but it actually tries to find the best fitting function that suits your data. I love it, and used it extensively in my latest works. It is called Eureqa.

Stay tuned!

 
 

Comments  

 
+1 #1 Manuel 2011-05-18 16:10
Hi, great site.

I'm doing myself some research related to biofilms, but this time I only wanted to comment about tools!

Tried TeXmaker? I have been using it for a time now and find it good, but never used LyX. Have you used both? How do they compare to each other?

Thanks for the great site again.
Quote
 
 
-1 #2 Danial 2011-05-18 20:24
Hi Manuel,

Thanks. I worked for years as programmer, so I do like LaTeX a lot. Nevertheless, LyX so easy to use that I don't have to code all the TeX stuff the way you do in TeXmaker. And, you see what you've done, like a light preview. The environment is quite powerful, and you can easily extend it like you do with any TeX doc.

Try it, it will ease your life a lot.


Quoting Manuel:
Hi, great site.

I'm doing myself some research related to biofilms, but this time I only wanted to comment about tools!

Tried TeXmaker? I have been using it for a time now and find it good, but never used LyX. Have you used both? How do they compare to each other?

Thanks for the great site again.
Quote