Forum: (Closed) How to get Biostar Handbook for free. And participate in building a better educational platform.
gravatar for Istvan Albert
2.3 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

This is a followup post to The Biostar Handbook. A bioinformatics e-book for beginners. and I would invite discussions and comments on the process or content here rather than on the announcement post.

Teaching bioinformatics data analysis and writing the Biostar Handbook clarified a lot in my mind about what bioinformatics is, what biologists need to know, and how to get there.

The main challenge is the rapid evolution (and decay) of methods and know-how. Bioinformatics is not suited at all to the traditional teaching methods where the actual content of most books don't have to change for decades.

This is what I am trying to achieve with the handbook - it is "living" book, one that may look very different next year, but it will also work like a software. In the future you can roll back to the good old 2016 to look at the same type of data analysis and say, wow I can't believe we used to do THAT.

You can be a part of this, you can join this effort. We are doing it either way. It is time to fix the way we teach bioinformatics.

Volunteer to contribute to the handbook and you get access to it right away for free. Become a regular contributor and you'll become someone with a weight and an influence on what we do and how we do it. I want to build an organization, Biostar, to be like Software Carpentry but one that focuses on bioinformatics training, certification, education and community.

We have many components working well. Biostar was a forum I built for a bioinformatics class that I was teaching. Students would hang out here during the semester then move on. Today, seven years later? Look at the bottom left corner, 1676 IP addresses visited in the LAST hour.

The same story will play out with the Biostar Handbook - I built after five years of teaching bioinformatics and finally it coalesced into what I think is and can be the best resource of this kind. It has many flaws and we'll be working to correct them it will take some time, but everyone that bought the book will benefit from that.

If you want to contribute send me an email and we'll add you to our team and you'll get access to the repository that stores contributions. You can do big things or small, just proofread (provided you are skilled enough) - that's extremely valuable as well. In general I invite everyone to think if they would like to participate.

In way this is sort of a mixture of startup + kickstarter.

handbook biostar forum • 5.3k views
ADD COMMENTlink modified 2.3 years ago by shreve69710 • written 2.3 years ago by Istvan Albert ♦♦ 79k

Guess I missed it! Happy to help in other ways as well!!

ADD REPLYlink written 2.3 years ago by Khader Shameer18k

Thanks Khader! We want your input ;-)

ADD REPLYlink written 2.3 years ago by Istvan Albert ♦♦ 79k

I've already read sections of the handbook from the previous thread, and immediately it was obvious that you're on to something here. The handbook is practical and very clear, particularly to biologists. I would be more than happy to help any way that I can :)

ADD REPLYlink written 2.3 years ago by John12k

Sounds great John!

A detail I forgot to mention. Everyone wanting to contribute send your Github ID to me at

And please do chime in here as well so that people know whose is on. Ram is on board as well.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Istvan Albert ♦♦ 79k

Wasn't following this thread so I did not see this comment. Everyone, yes, I'm in. In fact, I've pushed in a few commits and have gotten a few PRs pulled in - love the frenzy on this at the moment :)

ADD REPLYlink written 2.3 years ago by RamRS20k

Sent you an email.. I'd love to contribute my part

ADD REPLYlink written 2.3 years ago by roy.granit790

I contributed my first part today and more will follow. Great format!

ADD REPLYlink written 2.3 years ago by WouterDeCoster37k

This offer is now closed. At this point we have sufficient number of volunteers and I am afraid we can't accommodate everyone as it will be too difficult to manage everything.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Istvan Albert ♦♦ 79k
gravatar for ksaville
2.3 years ago by
ksaville20 wrote:

I am currently on sabbatical from a small liberal arts college. One of my goals for sabbatical is to develop a bioinformatics course. I've been thinking about/exploring various approaches and stumbled on this handbook today. I've made good progress getting everything installed and would be happy to provide feedback as I go through the materials if you think this perspective would be useful. I don't yet have a github ID but will sign up for one and send an email.

I already bought the handbook, so am not worried about the free access

Ken Saville

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by ksaville20

Excellent idea! Please do sign up. It is very difficult to reproduce that "first" user experience on our systems that we use for other tasks.

ADD REPLYlink written 2.3 years ago by Istvan Albert ♦♦ 79k
gravatar for shreve697
2.3 years ago by
shreve69710 wrote:

I am an environmental engineering PhD student interested in microbial communities and bioinformatics. I am currently undertaking a metabarcoding study looking at fungal (ITS) and bacterial/archaeal (V4) communities in various treatment processes. I will be submitting samples for sequencing on an Illumina MiSeq soon.

Does this handbook offer any introductory material related to metabarcoding studies?

ADD COMMENTlink written 2.3 years ago by shreve69710

At this moment it does not. You will find related threads and other resources on the net though.

ADD REPLYlink written 2.3 years ago by genomax64k
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