Wolfram mathematica in bioinformatic.

Question

[dshulgin]

Hi, biostars

I'd like to know if Wolfram Mathematica is used in bioinformatics/computational biology? For which problems?

Thanks

[Madelaine Gogol]

I know a mathematician who uses mathematica a lot. He does more heavy math modeling of biological systems type work. (edited to add -- Oh, I guess he helped DEVELOP it, so that makes sense).

Answer 1

[ablanchetcohen]

It is only used by those with no background in bioinformatics, but expertise in Mathematica, who decide to tackle a bioinformatics problem.

Proprietary software is rarely used in bioinformatics, and rightly so.

The statistical analysis language of choice in bioinformatics is R, which is completely open source, and has an extensive bioinformatics library of programs.

Answer 2

[DG]

Short answer would probably be Yes, but not be a very large number of people. Every once in awhile I come across some bit of code someone describes in a paper and it is Mathematica or MatLab and I promptly stop reading because neither are widely used. Unless you're really invested in Mathematica it isn't worth learning solely for bioinformatics (you may find other uses for it perhaps) and definitely not for publishing methods...

[dshulgin]

Actually, i'm not interested, i've got Mathematica course in my masters, so i wanted to know if it can be really helpful for bioinf. Thanks.

Answer 3

[dariober]

There are quite a few branches of biology that make heavy use of mathematics and hence where Mathematica is popular. For example ecology, evolution, population genetics, epidemiology. The book A Biologist's Guide to Mathematical Modeling, which is very good and written by expert in the field, has practicals written in Mathematica.

In any case, I don't know Mathematica at all but I feel quite confident in saying that once you get the hang of mathematical modelling then it should be fairly easy to switch to other platforms to implement it. I mean, the difficult bit is to understand the mathematics, the coding part is usually easier!

[ablanchetcohen]

I think there has been an evolution in mentalities towards open source software programs since 2007, when this book was published.

Tthe general, emerging, consensus in bioinformatics is to systematically favor open-source over commercial programs. You'll find a book on a similar topic written for R, that seems to sell better. Ecological Models and Data in R.

I've had similar debates over the merits of MatLab vs R. Unless there is extensive prior expertise in a commercial software program, for example, an engineer with decades of experience in Matlab, or some irreplaceable feature, for example the ease with which one can generate GUI in MatLab, open source software is always the best choice.

Dealing with licences is expensive and an unnecessary complication. It also slows down scientific progress since those without access to the licence can not verify the source code, or improve on it.

[dariober]

Dealing with licences is ... unnecessary complication Yes, I completely agree with this! However, let's keep in mind that R and mathematica are quite a bit different. In particular, mathematica can do symbolic maths which R can't. A nice open source platform for symbolic maths I played with is sympy.

[DG]

I did my PhD in molecular evolution. It is the only time I ever came across Bioinformatics papers published using either Mathematica or MatLab code, but even then it was on the way out. There may have been some more math oriented people using it but all of the heavy statisticians where generally using R or writing their own numerical code in C and Fortran. It was exceedingly rare even then (2006-2012)