Hi Biostars,
I am looking for an open source software that has been widely used in the past and current with biologist, I am a software graduate student and my main focus is on scientific software testing. Greatly appreciate if you can name some of the open source commonly used software in your community?
Edit: So the main purpose of this query "Finding the most commonly used software" is to run some software tests on source code and see if we can help and improve open source software.
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Eva_Maria
Have a look at the Biostars tags: https://www.biostars.org/t/ and try to extract only those tags which are software:
Then you get
But R and Python are also programming languages (and have an 'unfair advantage') which you can do a lot of different things with, therefore blast is - not surprisingly - the tool Biostars' users have most questions about.
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Michael Dondrup
Sorry, I closed this by mistake, it is open. I would consider using the Biostar tags also as another source of input. My usage is definitely not representative.
The top 5 software tools I use are different between mapping software and the top 5 differential expression software tools I use and etc.
I prefer command line tools so I don't use Galaxy, and I don't use blast very often but I know it's very popular.
To add one more data point to your survey, here's my selection from top of my head
I deliberately left out general purpose tools like R, python, unix command line tools etc.
Take a look a the Nature's top 100 for a historical view: http://www.nature.com/news/the-top-100-papers-1.16224
Interestingly, the Clustal W paper is ranked above BLAST, though there are several BLAST and Clustal papers so I think BLAST is collectively higher. Either way, both have had a large impact on the field but timing is a major factor in popularity, especially in the citation statistic.
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