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Forum: bioinformatics study partner

looking for a bioinformatics , SE, study partner for working together, skype: karimse07, email : karimse07@yahoo.com, facebook : Bioinformatics study partner

research study-partner
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updated by Ram Ram • written by karimse07 • karimse07

Hi karmise,

I'm really interested to work with people, but what is your mean about SE? what would you like to do?

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updated by Ram Ram • written by seta seta

I'm interested as well - what do you mean "SE"?

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updated by Ram Ram • written by bkolends • bkolends

Bioinformatics is a huge field. You might get better results if you specify exactly what you're focused on at the moment.

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written by Dan D Dan D

In principle a very good idea, you could try to solve assignments together, check each other's code, learn about the other partner's curriculum, exam questions, share rants etc. I think it would dramatically help to provide information on where you are, which courses you are enrolled in, which semester, etc. It is also extremely helpful to form local study groups for different courses.

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written by Michael Dondrup Michael Dondrup

Good idea. I am working on some open source projects. Looking forward to interact with like minded individuals.

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updated by Ram Ram • written by balkiprasanna1984 • balkiprasanna1984

2 answers

Hi all, bioinformatics is a huge field. A lot of information that makes hard to be very comfortable with the domain.

Despite me, I have a dental doctor degree, so, I have studied enough molecular biology and all related health fields (like pathology, immunology, etc). I hold a programmer degree at tech level. My domain is web app for bioinformatics. In my opinion, the present and the future will be web, will be browser. Means, I think in the near future we will be push to use tools like AWS and Google Cloud Platform to run our codes in Perl, Python, Bash, R, etc, in the cloud, and display our results in the browser. So I think JavaScript and its libraries like jQuery, D3.js, Angular, CIRCOS, ItOL, jsPhyloSVG, etc, and web development languages and techniques will be the core components to a bioinformatics filed. As a clinician professional, and bioinformatician I would like to solve one question: "How to make bioinformatics accessible in the real world for doctors. How (or when) the bioinformatics information or tools will be available to help doctors (that don't know nothing about programming) and patients outside from research world? That means, bioinformatics in practice for health professionals.". Once again, browser is a inconturnable reality.

So, I want to spent my time to learn everything as I can and exchange, change and create ideas in this direction, and I think, create a study group or partner is a good start. My e-mail is igoralves1@hotmail.com.

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updated by Ram Ram • written by YOT • YOT

I have to disagree with the web part of your comment. The web can never be the be all and end all of a data intensive field. True, one will use AWS for compute intensive analysis, but that is only because local machines cannot be scaled up and down on demand like cloud infrastructure. Pay-per-use can be a good model for a small to medium sized lab.

Ultimately, be it a local machine, an HPC or the cloud, we will need command line tools that do the actual task. Visualization might be over the web, but actual processing has to be at the command line.

And IMO, genetic counselors will benefit more from bioinformatics than actual doctors. Tapping into bioinformatics at a level that can be useful for patients needs an individual-oriented approach, and doctors usually focus more on the medical aspect than on the research aspect. GCs on the other hand are definitely more personal.

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written by Ram Ram

Hi RamRS,

Back in 1979, nobody in the world, could say that we could buy things around the world from our home, sit in our chair.

As a doctor, and as a bioinformatician I could guarantee you that generally 95% or more, of doctors don't know almost nothing about programming.

I would like to use your phrase "processing has to be at the command line". I don't believe that. You can see Bill Gates and Microsoft and DOS. Everything before Bill Gates was in command line. What I am trying to say is everything in bioinformatics must to be like "windows", by btn. Bioinformatics in the research world is not the same as bioinformatics in practical world.

The process part of the pipeline, must to be in a scalable computer but the results and the commands must to be in a browser. As a clinician I could say that the bioinformatics didn't arrived at offices yet.

And who that will be the first to understand that will be the next Bill Gates.

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updated by Ram Ram • written by YOT • YOT

Well, I'm not going to discourage your vision, but I for one am a bit more grounded. I know that cloud solutions to a lot of command line problems exist, and I know that there might a breakthrough some day that might make command line obsolete, but I do not see any such event in the horizon and I'm quite sure abandoning command line learning is not gonna result in a web boom.

And if you noticed the trend in bioinformatics, we have been going from the "Windows way" (point and click) to the "Unix way" (command line) - NCBI's BLAST is an amazing example of that. Open source lends itself to creative modifications of existing tools and a point-and-click abstraction does not work well with that. And, Gates made Windows with an immense mastery over the existing UI, not by denouncing it.

And like I said, doctors do not need to know programming. Bioinformaticians and genetic counselors exist for a reason.

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written by Ram Ram

This is what I was trying to say:

  • How to better understand the challenges and eliminate bottlenecks that are limiting the success of whole genome sequencing in the clinic.
  • How to overcome the knowledge gaps and specific technical issues that might help you push forward with your own clinical whole genome sequencing.
  • How to interact with patients and patient advocates to address any concerns they might express about having their genomic profiles characterized in a clinical setting.
  • What are the pluses and minuses of specific instruments currently being used to carry out whole genome sequencing.

Source: http://www.genengnews.com/webinars/taking-whole-genome-sequencing-into-prime-time-clinical-practice/242/

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updated by Ram Ram • written by YOT • YOT

Let us agree to disagree, then. Like I said, I think your vision is great, but I also think that the path to seeing it materialize will involve a group of command line experts at the core who will make the pipelines tweakable black boxes for clinical doctors - think Galaxy, but more abstract.

"Everything on the web" will in fact be layers upon layers of shell, cmake, Java, Scala and such automation scripts structured to make analysis feel smooth and abstract the details from the lay user.

Once again, my point is not that WGS won't be accessible to doctors, it is that web cannot the be all and end all of the future.

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written by Ram Ram

Hi all, could you please add me as your group. I can do with RNA-seq, Chip-seq with Tophat, cufflinks, R, Linux..

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written by quangmaiv • quangmaiv

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