The Biostar Handbook collection now includes five volumes of straight-up, no-nonsense data analysis from the trenches!
- March 2023: The Biostar Workflows has been expanded . Added the 10-minute RNA-Seq chapters.
- November 2022: The Art of Bioinformatics scripting has been modernized.
- April 2022: A new volume: Biostar Workflows in the seriers. Learn how automate bioinformatics analysis
- March 2021: A new volume Coronavirus Genome Analysis. Learn about viral genome analysis.
- January 2020: A new volume RNA-Seq by Example. Detailed step by step guides to RNA-Seq.
- May 2019: A new volume **The Art of Bioinformatics scripting released. Lear how to script like a pro.
- January 2018: A rewrite of the Biostar Handbook. New installation instructions, many chapters rewritten.
All new content is always included with the subscription.
December 1st, 2016: Original Announcement
Announced almost 18 months ago, the Biostar Handbook has now been published. It delivers simple, concise, and relevant information for those looking to understand the field of bioinformatics as a data science.
It is a comprehensive, practical handbook that aims to cover (though it is not quite there yet) all major application areas of bioinformatics.
- Read the Biostar Handbook
- Get the Biostar Handbook
Special thanks go to Biostar users GenoMax , shenwei356 and Jeremy Leipzig who have contributed entire pages or sections to the book.
Only now that the book released - as I am looking at 713 pages of do I start to realize just how big Bioinformatics has gotten in the past few years. And we're still missing entire subdomains of it: Metagenomics, Assembly, ChIP-Seq. But fear not we'll handle those too in this coming year.
Spread the word, let others know - I think there is no other resource like it. I like to call it data analysis with attitude, where reproducibility means not following letter by letter, but doing it better, faster and simpler.
Let me invite anyone that wishes to contribute to do so. It is easy, and simple, Markdown based publishing. And there is so much more that could be done and will be done. Be a part of it! We are independent, self published, self supported. Chart your own course, bring your own ideas and goals to fruition or just enjoy being a part of a creative process.
Please join me in Congratulating @Istvan on this special day!
This will hopefully be THE bioinformatics information resource for both students and instructors (and anyone else who may be just curious). Looking forward to continued collaboration.
On thing I forgot to mention - everything in this book works on Windows as well! The new Bash for Windows subsystem worked amazingly well. Only
fastq-dumphad problems connecting.
I had been in contact with the Microsoft Genomics team and they reached out to the Bash Team - sure enough they put in a fix just to make
fastq-dumpwork for us. This will be pushed out in some of the updates to OS.
I was very impressed how well it all worked out on Windows as well.
May I know the way of contacting withthe Ubuntu Microsoft people? I am aware of some problems with another tools, such us fastx-toolkit
I have a personal contact that put me in touch so don't feel comfortable sharing that information.
As for the fastx-toolkit I would recommend not using it - it is not the right tool anymore.
I am not a fan of fastx-toolkit. It cannot work with more than one threat and it is slow.
But the point is that some error is there avoiding this program and maybe some other programs to work nicely with Window-Linux. I haven't tried the latest version, though..
what problems are you having with fastq-dump ? it works well on WSL in the insider preview windows version
Congratulations! So nice for you to make money from open source community efforts.
I understand the sentiment and why you would post this. I thought of this myself as well. The book even has a FAQ titled: Why isn't the book free? - in a nutshell, creative process is fun, cleaning up after other people's creative processes is hard work.
I understand the sentiment and why you would write such a FAQ, but I just do not believe you make the world a better place by selling information. The Internet is full of people who create things for free, no matter how much work they put in. However, it is not about the money you ask, it 's about using the name of a open source community (where a lot of people are willing to spent their precious time on helping others) to sell you product.
Content of the book is mainly based on a graduate course @Istvan has taught at Penn State for last few years.
AFAIK content of the book is freely accessible over the net (you only need to create an account). Only those wishing to obtain a PDF/eBook copy are expected to make a purchase.Rationale for that decision is described in the FAQ.
Disclosure: I did contribute some content to the book under the licensing described here without any expectation of financial gain.
So why call it the BioStars handbook and not the @Istvan Penn Stat course handbook? My guess is to make more money.
And I tried to make an account just now but I need to pay for the book to get one.
My apologies. I thought the online version was "free to access" but I was wrong. I have made a correction to my post above.
No sir, information will cost you $$$.
I am contributing to the initiative - both time and money. I've paid for the book and I'm going to be working on the content. To me, it's not about the money. $30 for 2 years' access is peanuts. I've always admired Istvan's efforts in building this community and a site that multiple communities could tailor to their use case.
I have a philosophy that I follow for this free/paid thing, especially for my favorite websites, YouTube channels and webcomics. If someone gave me access to their work for free, and they're selling an offshoot, I'll pay for it gladly. I want them to make a profit with their skills, I want to benefit from their skills - I don't want them to stop because it gave them no return.
If Istvan had asked for $10 a year to help maintain the site, I'd have paid it gladly.
Congratulations @Istvan. About to buy the handbook. Looking forward to having this on my desktop!
Thank's everyone for the encouragements. Proofreading is my bane - the hardest part for me to do for this book. So there are plenty of awkward sentences - but just about every day I push out more fixes to wording.
Now I could recommend my biology friends a one-stop solution to begin with bioinformatics. Thanks a lot Istvan (and others), for the efforts behind this book and ideas. I wish this was published when I started Bioinformatics.I am eager to read this book and learn more Bioinformatics.
Congratulations, stellar book with great content and elegant design. Will be ordering a print version - hope I can get a signed copy :)
No print version as of yet though, but come to think of it I can sign PDFs!
There are now 4 separate books in total, however, all the links lead to the index page of The Biostars Handbook so it's impossible to check what's inside each of them. I'd like to know what topics does the "Coronavirus Genome Analysis" cover. Could you please fix it?
This is a good suggestion. If it's not too much of a hassle, the index on the left should reflect chapter titles and sub-titles (maybe redacted a little) so people know what they're getting.
This particular book needs to be rewritten as NCBI has recently changed the way they distribute the data, hence invalidated a section that dealt with getting the data (genomes, sample metadata etc). The book will be rewritten with viral genome analysis in mind - a general topic, how to obtain and analyze viral sequences in general (the example applications to SARS COV 2).
Great resource, bought a copy and have been reading through it all day, lots of useful tips and explanations. Well done everyone involved.
Thanks James Ashmore we will keep at it, we will expand it - I predict doubling the content by Summer and always "keeping it real".
hello I've been using Biostars for 1 year so i bought the book , i will like to add if it is possible to add chapter about small RNA and long non coding RNA and how to analyze their data. also is it possible to add tips how to deal with non-model organism and how to annotate genome based on transcriptome. congratulation for this nice book.
Early next year we will send out a questionnaire for the readers to ask them what they want covered. And we will try add if not all but most of the topics people they want covered.
The Biostar Handbook is not the typical book where we put it out there, then walk away. That's really why I am doing this - I want a "living" book in a different kind of publishing system one that works like software itself. It adapts and changes with time, you can upgrade or use the prior versions.
Regarding licensing, would you entertain the option of an institute-level license? For example, we don't really need 5 copies of the book, but a single copy with either an institute-level account or allowing multiple accounts from the same institute would be really nice.
Everything is possible since I chose self-publishing :-)
Please send me an email and we can discuss this further that way.
Will do, thanks!
As a Bioinformatician with a short experience, I recognized myself very well in the short paragraph about stress and anxiety for the only analyst on a project. Just for this part I can say that the book reflect quite well the reality of the practice.
I bought it to learn more about domain in which I am not really familiar, but I am pleased to discovered things about the basics of bioinformatics that will help me in the future (the iteration over a stream open by cat to build a command).
My only grief is the change to the bash_profile in the "how to set up my computer ?" that turns my terminal to be ugly as hell and make me freak out for a minute ;p You should add a warning about this.
Thanks for the feedback.
For what is worth, I think that BASH prompt is best that I found - though I may have not properly explained why you'd want that information. I will be updating that section to include the following:
The bash prompt should give you information on the context that you are working on. Initially, when you only work on a single system and in a single directory the information seems unnecessary. As soon as you deploy across different systems it helps you avoid making the biggest mistakes you can make: running a command on the wrong computer or the wrong directory. You can do some lasting damages that way .... :-) most bioinformaticians have war stories to tell you about that ...
Thus the prompt is set up to continually, even obnoxiously, remind you of the following:
In addition, it opens a new line to avoid pushing the prompt too far to the right, so long commands will still fit without wrapping
cherish this information :-) on day it will save your bacon
Totally agree on the "be conscious of the computer, directory and user" point. Often times, you'd be working on a dev and a production server and you'd need to do some major operation on the dev server (such as clean up all logs) that would, if executed on the production server, wreak havoc.
Imagine managing an AWS server and having two logins, one with root privileges and the other a regular account. You're in a folder that has a sub-folder named
devand you wish to run
rm ./dev. You type the command, but make a typo and miss out the
.. It only takes a small coincidence to delete all the information you have on the server.
Even if one were super cautious to work without this "insurance", if not for this heads-up information, they'll find themselves running
pwdat least every other minute (best case scenario).
There is a warning, although it definitely is not prominent. The line after the
curlcommands points you to the "Setting the bash profile" page, which shows the exact file being used.
Also, one should never trust content from the internet implicitly. Always read the file you're
source-ing before you source it.
I don't understand how it turned the terminal "ugly as hell", by the way. The statement that alters the shell is the
PS1setting, and it adds some color to the display. What is your recommendation for warning the user about this change?
I have opened a new thread to channel discussions on the book there and keep this more focused on the announcement itself.
How to get Biostar Handbook for free. And participate in building a better educational platform.
Thanks! this is an excellent and relevant resource.
I was wondering what was your plan next. Will you add more softwares examples like PLINK! or GEMMA? Like more info on how to run a basic molecular ecology problem using GWAS?
The current plan is to cover various domains of applications over the next year. ChIP-Seq, small RNA and so on. We're interested in covering other software like PLINK as well.
Many congratulations on publishing the book, yet another feat you (other contributors) have achieved after the Biostars.org itself. I have advertised book to many people already who ask me on a daily basis how to start in Bioinformatics, clear, concise and to the point. Would love to contribute to the future episodes. xx
Congrats on your book Istvan!!!! Always love it!!!! :)
I think this was the best money I spent in some time. As someone who was totally unfamiliar with command line, I find that many guides assume too much baseline knowledge about how it works and move straight on to the tools. This book does a great job of introducing you to both at the same time. I might not be an aficionado yet, but I have made a lot of progress in a short time, and am gaining confidence in working outside of the security of the book's instructions. Thank you to all the authors for their continued efforts!
Thank you for sharing your experience. I am always thrilled to hear that the book "works" in practice :-)
thank you for sharing your experience but I can't login to read the book!! Is biostar username and password valid?
Did you receive the credentials in your email? I'm assuming you already paid for it.
The book is independent of this website and is not a free resource. This is where you can purchase the book:
whats the difference in the content of the 25$ and 35$ handbook? I want to buy one nd dont know what the dfference is.
It clearly mention in the picture: The $25 gives you access to the book for 6 months; the $35 gives you access for 2 years.
I know all that. Im talking about the content. whats inside? I am just wanting to know if the content is the same. thats all.
There is only one version of the book as far as I know. So the content should be the same.
It's a little difficult to find, but the book is web-based and is continually updated with the latest and evolving best practices in the field. That's the reason the sales model behind the book is time-based and not content or copy-number based. The idea is that when you wish to work on/learn a particular technique, you'd learn the current best practice and not outdated tech. It's a continuous effort from the team behind the book, and that's why it's a per-block-of-time cost.
The content is the same at any given time point for both editions. Moreover, readers may keep the last PDF and eBook version they have access to. Thus student edition owners would get access to the version released six months from now as well. What they would not be able the access is the website and the new edition say seven months after their purchase.
Hence the differences will only appear in time, as new content gets added. For a list of new content that was added:
Plus in the past year, an online course was added with another to follow. These are all web-based, so access to these are limited by the subscription terms.
What is the best way to report typos in the handbook? shall I open a gihub issue? Any specific format for the same?
Create an issue: https://github.com/biostars/biostar-handbook-issues/issues
If there are multiple include them in a single post.
Looks amazing, I will probably get this to get everything on a single book before starting my PhD. May I ask if you plan to do something on ATAC and Hi-C as well? What about sc Sequencing? It's already huge, I just hope to see those features in future. Great job and keep going!
Single cell sequencing is a topic I would like to add - but the field feels quite un-settled: for example, which RNA-Seq should we use? ... fifty publications later, well well well maybe we should use the same as regular RNA-Seq... really? hard to believe...
All content in the book comes from personal hands-on experiences - hence I need to get involved a little more myself.
@Istvan Albert How can i get This book Plz...???
The link is in the post :-)
I bought the course last month and it's fun and informative. Thank you for updating the content.
I am trying to get my college to buy this book and courses for bioinformatics students.
I'd like to know please:
While @Istvan will likely respond, you should email contact at biostarhandbook.com with questions.
As genomax points out the right email is
A short answer is that everything is included.
Thanks for your fast replies
Hi, Some small things I found that need to be corrected. In chapter "common data types", the first paragraph ends incompletely. Also, in the same chapter the title "Is there a list of “all” resources?" is repeated from the previous chapter.
Please use the issue tracker for biostar handbook for to create a new issue for these corrections.
A nice book. Thank you Istvan!
Is The Art of Bioinformatics Scripting different from the Biostars Handbook ?
Yes. It is a new book that is included as a part of your subscription to Biostars Handbook.
Yes, as genomax points out, it is included with the Biostar Handbook.
The content in the *The Art of Bioinformatics Scripting * started out as a chapter in the Biostar Handbook, but then in time it has grown enough to warrant moving it into a separate book.
@Istvan Albert how to get such books please ??
You have to purchase access. It is subscription based. All materials are included in one subscription.
@genomax well, so please share the subscription link
It takes less effort to click on any handbook link on the top level post and the click the "Get access to the book" green button than it takes to ask others to do the work for you and give you a direct link.
The first rule of seeking help anywhere is to invest some effort yourself.
@Istvan many congratulations for this great resource. Wishing you a great success.
Hi, I'd like to buy the biostar handbook with title "Corona Virus Genome Analysis". However, I do not have the payment methods listed in the link. Is there a way to get around then? Any comments are greatly appreciated.
There is a single "subscription" price for the "suite" of books/training materials. You have to buy that subscription.
Could you kindly let me know how to proceed ?
Buy the book at this link.
I tried this earlier and did not buy because I do not have the payment methods...
@Istvan Albert There should be a dedicated part in the upcoming version of the book for sequencing analysis results visualization, which covers circos, heatmaps, and other visualization methods.
Great! Thanks for the book!
First thing I read was section on "how not to waste your time". I agree totally wrt Docker and push button type cloud compute environments. The CWL section was hilarious.
This will hopefully be THE bioinformatics information resource for both students and instructors (and anyone else who may be just curious). Looking forward to continued collaboration.