Question: What Software Programs Do Bioinformaticians Need?
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gravatar for harold.serrano
6.4 years ago by
harold.serrano10 wrote:

Hi, I'm very well verse in computer science. The languages which I'm very comfortable with are C++, Java, objective-C. I'm catching up on bioinformatics. I honestly know very little. I'm very interested in developing programs for bioinformaticians to use. However, since I'm not in that field, I don't know what is what they need. Can anyone tell me what kind of software programs most bioinformaticians need? What kind of software they wish was around?

Thanks

software programming • 2.6k views
ADD COMMENTlink modified 6.4 years ago by KCC3.9k • written 6.4 years ago by harold.serrano10
8
gravatar for Gabriel R.
6.4 years ago by
Gabriel R.2.6k
Center for Geogenetik Københavns Universitet
Gabriel R.2.6k wrote:

This is akin to going on:

http://cooking.stackexchange.com/

and asking what sort of ingredients do chefs use ?

:-P

ADD COMMENTlink written 6.4 years ago by Gabriel R.2.6k

Wow!!!!!!!!!!!!

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by harold.serrano10
1

My comment was just meant to illustrate the eclectic nature of the field. People that work on RNA structure prediction, high throughput sequencing, databases for system's biology, theoretical aspects, phylogeny etc will use vary different software, there is no software that is a sine qua non for being a bioinformatician.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Gabriel R.2.6k
1

Ok thanks. I'm new at this, so I was looking for a more concrete answer. But I do understand what you mean. I should have been a bit more specific.

ADD REPLYlink written 6.4 years ago by harold.serrano10
2
gravatar for Irsan
6.4 years ago by
Irsan7.0k
Amsterdam
Irsan7.0k wrote:

samtools, bedtools/bedops, picard tools, vcftools, bcftools, bwa, blast, ggplot (R library)

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Irsan7.0k

Thanks, that was helpful.

ADD REPLYlink written 6.4 years ago by harold.serrano10
2

All those programs are great for people who work with Next Generation Sequencing, but NGS isn't the be-all-end-all of bioinformatics. Not by a long shot.

ADD REPLYlink written 6.4 years ago by swbarnes26.5k
2
gravatar for KCC
6.4 years ago by
KCC3.9k
Cambridge, MA
KCC3.9k wrote:

First, there was a recent post on what people spend a lot of their time doing as bioinformaticians. It was called What Do You Waste Your Time On. You might get some ideas there.

Second, there is a high level of programming ability in the bioinformatics community. So, many are used to just scripting whatever they need. In a lot of cases, the end users of bioinformatics software are other programmers. So many programs never get very much polish because the users can usually hack them into something usable without a lot of handholding. Two addition causes of gaps in available software are that the technology keeps changing, making old software obsolete and necessitating new versions, and that most bioinformaticians work in an academic environment where inventing new things is rewarded and maintaining old things is not. I bring all this up so you can a sense of what the bioinformatics software ecosystem is like since you are thinking of getting involved.

Third, my suggestion for a cool project that would be tremendously helpful and accessible to the beginner is writing a program that can easily translate between a large number of bioinformatics data formats. There are a few programs that do some conversions, but no single program that does the vast majority of conversions between say: bed, bedgraph, fixed wiggle, variable wiggle, bigwig, bigbed, sam, bam, fastq, fasta. This is a tremendous amount of work though.

ADD COMMENTlink written 6.4 years ago by KCC3.9k

Thank you, I will look into that.

ADD REPLYlink written 6.4 years ago by harold.serrano10
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