News: The Biostar Handbook. A bioinformatics e-book for beginners.
292
gravatar for Istvan Albert
3.0 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

November 1st, 2019: The Art of Bioinformatics Scripting

The Biostar Handbook has grown huge :-) it is now close to 1000 pages! To manage this complexity we have started reworking the various chapters into independent books.

Bioinformatics Data Analysis

The reorganization will allow readers to more easily locate the information that they need. It will allow us to design and formulate specific training plans that are customized to specific needs. The first book section that has been reworked covers Unix Scripting and is titled:

As always all new content is included with your subscription.

January 2019: Biostar Handbook 2nd Edition, New Online Course

A little more than two years after the launch, the Biostar Handbook gets a rewrite. The 2nd Edition is a complete rework, every section, chapter and page will be edited, expanded and modernized. A new course has also been launched as part of the book:

The Learn Bioinformatics the Right Way course is included with the book at no extra charge. The course is well-suited as an introduction to this field of science, or to brush up on topics you have learned before.

Bioinformatics Data Analysis


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.

enter image description here

It is a comprehensive, practical handbook that aims to cover (though it is not quite there yet) all major application areas of bioinformatics.

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.

handbook training news tutorial • 44k views
ADD COMMENTlink modified 8 hours ago • written 3.0 years ago by Istvan Albert ♦♦ 81k
20

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.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax74k
6

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-dump had 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-dump work 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.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k
1

May I know the way of contacting withthe Ubuntu Microsoft people? I am aware of some problems with another tools, such us fastx-toolkit

ADD REPLYlink written 2.9 years ago by Antonio R. Franco4.2k
1

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.

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 81k

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..

ADD REPLYlink written 2.9 years ago by Antonio R. Franco4.2k

what problems are you having with fastq-dump ? it works well on WSL in the insider preview windows version

ADD REPLYlink written 4 months ago by Elephantdumbo20
5

Congratulations! So nice for you to make money from open source community efforts.

ADD REPLYlink written 3.0 years ago by Zaag720
8

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.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Istvan Albert ♦♦ 81k
4

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.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Zaag720
2

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.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax74k
6

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.

ADD REPLYlink written 3.0 years ago by Zaag720
1

My apologies. I thought the online version was "free to access" but I was wrong. I have made a correction to my post above.

ADD REPLYlink written 3.0 years ago by genomax74k
3

No sir, information will cost you $$$.

ADD REPLYlink written 3.0 years ago by Zaag720
10

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.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by RamRS24k
3

Congratulations @Istvan. About to buy the handbook. Looking forward to having this on my desktop!

ADD REPLYlink written 3.0 years ago by avismirabilis40
1

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.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k
2

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.

ADD REPLYlink written 3.0 years ago by venu6.3k
1

Wonderful, congrats!

ADD REPLYlink written 3.0 years ago by Anima Mundi2.5k
1

Great resource, bought a copy and have been reading through it all day, lots of useful tips and explanations. Well done everyone involved.

ADD REPLYlink written 3.0 years ago by James Ashmore2.7k
1

Thanks James Ashmore we will keep at it, we will expand it - I predict doubling the content by Summer and always "keeping it real".

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k
1

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.

ADD REPLYlink written 3.0 years ago by najibveto40
1

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.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k
1

Congratulations, stellar book with great content and elegant design. Will be ordering a print version - hope I can get a signed copy :)

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Khader Shameer18k
3

No print version as of yet though, but come to think of it I can sign PDFs!

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 81k
1

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.

ADD REPLYlink written 2.5 years ago by Devon Ryan92k
1

Everything is possible since I chose self-publishing :-)

Please send me an email and we can discuss this further that way.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Istvan Albert ♦♦ 81k
1

Will do, thanks!

ADD REPLYlink written 2.5 years ago by Devon Ryan92k

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.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k

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?

ADD REPLYlink written 2.9 years ago by beausoleilmo260
1

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.

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 81k

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

ADD REPLYlink written 2.9 years ago by Sukhdeep Singh9.9k

Congrats on your book Istvan!!!! Always love it!!!! :)

ADD REPLYlink written 2.4 years ago by blairzxy30

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!

ADD REPLYlink written 2.1 years ago by hermoinejean0

Thank you for sharing your experience. I am always thrilled to hear that the book "works" in practice :-)

ADD REPLYlink written 2.1 years ago by Istvan Albert ♦♦ 81k

thank you for sharing your experience but I can't login to read the book!! Is biostar username and password valid?

ADD REPLYlink modified 23 months ago • written 23 months ago by mohammadhassanj70

Did you receive the credentials in your email? I'm assuming you already paid for it.

ADD REPLYlink modified 23 months ago • written 23 months ago by RamRS24k

The book is independent of this website and is not a free resource. This is where you can purchase the book:

https://biostar.myshopify.com/

ADD REPLYlink written 23 months ago by Istvan Albert ♦♦ 81k

whats the difference in the content of the 25$ and 35$ handbook? I want to buy one nd dont know what the dfference is.

ADD REPLYlink written 19 months ago by jaqx00860
1

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.

Biostar Handbook screenshot

ADD REPLYlink modified 19 months ago • written 19 months ago by RamRS24k

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.

ADD REPLYlink written 19 months ago by jaqx00860

There is only one version of the book as far as I know. So the content should be the same.

ADD REPLYlink written 19 months ago by genomax74k

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.

ADD REPLYlink written 19 months ago by RamRS24k

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:

https://www.biostarhandbook.com/public/updates.html

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.

ADD REPLYlink written 19 months ago by Istvan Albert ♦♦ 81k

What is the best way to report typos in the handbook? shall I open a gihub issue? Any specific format for the same?

ADD REPLYlink written 18 months ago by lakhujanivijay4.5k

Create an issue: https://github.com/biostars/biostar-handbook-issues/issues

If there are multiple include them in a single post.

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax74k

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!

ADD REPLYlink written 17 months ago by franc.jian40
1

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.

ADD REPLYlink written 17 months ago by Istvan Albert ♦♦ 81k

@Istvan Albert How can i get This book Plz...???

ADD REPLYlink written 11 months ago by Chaimaa150

The link is in the post :-)

https://biostar.myshopify.com/

ADD REPLYlink written 11 months ago by RamRS24k

I bought the course last month and it's fun and informative. Thank you for updating the content.

ADD REPLYlink written 8 months ago by Glory Basumata140

Hi,

I am trying to get my college to buy this book and courses for bioinformatics students.

I'd like to know please:

  1. The Bioinformatics Data Analysis course mentioned above is not mentioned on the site when buying the books. Is it still included with every purchase?
  2. The student pack doesn't mention access to the Python course. Is that not included with the students pack?
  3. For further questions in this regard, who can we contact?

Thanks.

ADD REPLYlink modified 5 months ago by RamRS24k • written 5 months ago by Malka20
1

While @Istvan will likely respond, you should email contact at biostarhandbook.com with questions.

ADD REPLYlink written 5 months ago by genomax74k
1

As genomax points out the right email is contact@biostarhandbook.com.

A short answer is that everything is included.

ADD REPLYlink written 5 months ago by Istvan Albert ♦♦ 81k

Thanks for your fast replies

ADD REPLYlink modified 5 months ago • written 5 months ago by Malka20

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.

ADD REPLYlink written 3 months ago by Cdk0
1

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:

  1. What computer and what user are you logged in as
  2. What directory are you currently in

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

enter image description here

ADD REPLYlink modified 3 months ago • written 3 months ago by Istvan Albert ♦♦ 81k

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 dev and 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 pwd at least every other minute (best case scenario).

ADD REPLYlink written 3 months ago by RamRS24k

There is a warning, although it definitely is not prominent. The line after the curl commands 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 PS1 setting, and it adds some color to the display. What is your recommendation for warning the user about this change?

ADD REPLYlink written 3 months ago by RamRS24k

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.

ADD REPLYlink written 6 weeks ago by Parham1.4k

Please use the issue tracker for biostar handbook for to create a new issue for these corrections.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax74k
7
gravatar for jiwpark00
3.0 years ago by
jiwpark00200
jiwpark00200 wrote:

Congratulations! I've been using Biostars for past 6+ months so I just bought the book. I'm intermediate-savvy with bioinformatics (I can usually figure out what to do if I search on Biostars or Google but I don't know all the codes off my head) so this book will be great in getting my skills up-to-date.

I already like that you included a section of Unix commands - that's something a lot of bioinformatic workshops don't go in enough depths about.

What would be the best way for contributing? Does GitBook work like Github? I think it would be great if there is a section on maybe WGCNA (or at least mention it). Maybe this is not applicable to everyone but majority of people I've talked to (and many are wet-lab biologists) really want to be able to take RNA-seq data and put into WGCNA but tutorials available are pretty abstract (UCLA tutorial requires some experiences, for instance).

Overall an amazing tool! It's like an early Christmas gift :-)

ADD COMMENTlink written 3.0 years ago by jiwpark00200
1

I am planning to do a tutorial and vignette of WGCNA later on after refactoring a little bit the code. I am adding test and updating the package in this github repository https:github.com/llrs/WGCNA.

ADD REPLYlink written 2.9 years ago by Lluís R.870
5
gravatar for Baby Bioinformatician
7 months ago by
Moscow
Baby Bioinformatician70 wrote:

A huge metagenomics project in my Lab failed just because my boss refused to employ a bioinformatician. Of course I didn't know anything in bioinformatics apart from the word itself, so I couldn't save the project.

Then I decided, even if it means life or death, am gonna settle down and learn bioinformatics. Yes, I got started, and day by day, my confidence is growing steadily thanks to "The Biostar Handbook" which I purchased 3 months ago. I think we need to add something like "Teach Yourself Bioinformatics" to the title of this book, because for sure, that's what am doing with this book. I would highly recommend it for anyone passionate about starting a career in bioinformatics.

And I must say that I would even pay more for it because the information in there is not just worth those peanuts you pay to get the book. It's worth a career! And now there is also this huge Biostar community with answers to almost every question I as a starter may have, and you get these answers instantly as if there is a robot sitting on the other side with answers ready to respond to your questions. This gives you the feeling that not matter what, you will always get the help you need.

Then there are these guys complaining that the "book should have been for free", and those claiming that the "Biostar community is diminishing the power of Bioinformatics cores". Come on guys, give us a break. You buy a book for only and only $35 and enjoy all those privileges for two good years and you can't say thank you? This is ridiculous!

ADD COMMENTlink written 7 months ago by Baby Bioinformatician70

Glad to hear that it worked out for you.

Adding the subtitle that you suggest is a great idea - I do think that the book is an efficient way to learn bioinformatics from first principles. The second edition is now getting close to release - I'll consider adding the "Teach Yourself Bioinformatics" as a subtitle.

You are also right on the money with the observation that the book teaches skills that can form the basis of a career!

Thanks again for the kind words and welcome to Biostars!

ADD REPLYlink written 7 months ago by Istvan Albert ♦♦ 81k
4
gravatar for Istvan Albert
2.8 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

There is a GitHub repository that tracks issues, problems and suggestions for the book.

If you experience any type of technical problem please visit the site below to create a new issue.

https://github.com/biostars/biostar-handbook-issues/issues

ADD COMMENTlink written 2.8 years ago by Istvan Albert ♦♦ 81k
3
gravatar for Sentinel156
3.0 years ago by
Sentinel156120
Melbourne, Australia
Sentinel156120 wrote:

I've been following this for the last couple of months and really glad to see it released! It was an instant buy for me as a wet-lab phd student interested in bioinformatics. I was wondering if it is possible to supply an epub version alongside mobi for those without kindle e-readers? Also is there a plan to perhaps have an online repository on github or similar for code examples and workflows from the book? This could be similar to Vince Buffalo's Bioinformatics Data Skills book. Overall I can't wait to get stuck into reading it, i'm sure it will save me and many others hours of time searching for help online, so congratulations and thanks again to all involved for all of the hard work putting this together!

ADD COMMENTlink written 3.0 years ago by Sentinel156120
3

Great idea on the github repo. We'll do it - though might take until next year to deploy

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k
2

The epub versions have been now added. See also the update page:

https://read.biostarhandbook.com/public/updates.html

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 81k
1

Oh indeed my mistake I thought mobi will work on both. I can and will generate epub formats as well.

I am traveling ATM so I might not be able to do it until later tomorrow.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k
2
gravatar for june.shuer.deng
2.8 years ago by
june.shuer.deng20 wrote:

I am the first person in my lab to attempt bioinformatics analysis using command line (with zero training). This book has been extremely helpful, covering some important basic concepts and moves on the complex & practical analysis.

The most brilliant thing about this book, is that it is unbelievably fun to read! People in the office caught me laughing out loud while 'studying' bioinformatics several times. The author has a very interesting character! He is passionate about what he does, while occasionally pokes fun of the irrational reality. It really feels like having a tutor telling me things beyond the textbook. Thank you for making me clueless attempt surprising enjoyable.

ADD COMMENTlink written 2.8 years ago by june.shuer.deng20
3

Thanks for the feedback. Much appreciated! I was hoping to make learning more enjoyable and fun.

And, as you point out it was indeed one of my goals to get people to see the some of the idiosyncratic aspects of bioinformatics. With no doubt the field is home to geniuses when it comes to software development - yet at the same time a suspension of disbelief is necessary to deal with the emerging complexity caused by going forward too fast.

Laughing at it (or with it) is how we deal in our group.

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 81k
1
gravatar for Daniel
3.0 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

This looks great, impressed to see chapters dedicated to things that you can only usually get a handle on from hours or days of google-fu (was looking forward to checking out sratools, entrez and bioawk).

EDIT: I originally had a comment on empty sections, but I'm throwing it out because it's totally misleading. I was totally wrong, and as Istvan pointed out I've skipped straight over the section on analysis and inadvertently found myself in the tools section.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Daniel3.7k
3

I am not sure I follow. RNA-Seq has detailed sections in the book. There are 12 sections on RNA-Seq with very detailed instructions on how to perform the analysis. There are five different fully worked out examples from evaluating controls samples to two ways of doing the Zika analysis. It all starts here:

https://read.biostarhandbook.com/rnaseq/rnaseq-intro.html

The tool chapters as just how to install them and perhaps on how to test.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Istvan Albert ♦♦ 81k
1

I'm really sorry, as you've pointed out, I've scrolled through to the tool pages in the pdf without realising that I've passed over the instructional and data analysis sections. I'm going to edit my comment now.

A couple of suggestions would be maybe to rename "Using Tophat2", "Using Kalisto" to "Installing Tophat2", "installing Kalisto" etc, and maybe introduce a hard page break into the contents pages (Maybe number them appendices?) as I didn't realise that the sections had changed when scrolling through 10 contents pages.

It's my fault for skimming quickly though. Significantly more than I saw on first pass.

ADD REPLYlink written 3.0 years ago by Daniel3.7k
1

This is a good point - that naming is confusing I will change it and push the new version.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k
1

The naming has been changed to "Install" - new pdfs are available as well.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 81k

The same applies for every tool. The book is not tool centric - it is task centric.

We never want to use just use seqtk we always have problems that can be solved with seqtk.

One would only visit the dedicated seqtk page only when installing it first or to verify some limitation and problem that this tool might have. That is why each tool has a separate page - and sometimes that page is somewhat empty when the tool does not have many issues affecting it . Still worth having it on its own page as it makes locating it very easy via search. Just type seqtk in the search box and you'll get the pages

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Istvan Albert ♦♦ 81k
1
gravatar for ahramkim1128
2.9 years ago by
ahramkim112810
United States
ahramkim112810 wrote:

In https://read.biostarhandbook.com/ontology/sequence-ontology.html page, URL=https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so-xp-simple.obo curl $URL > so.obo doesn't work. There is no file in the URL. Please edit this in the next update version. :)

ADD COMMENTlink written 2.9 years ago by ahramkim112810
1

Please try this URL instead. We will correct it in the book.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax74k
2

Goes to show just how links "rot" within a month or two. Starting with next year we will do nightly builds of all code in the book - I now realize that the book itself needs to be treated as if it were software - needs to be re-built every day (or perhaps every hour)...

The link has now been fixed in the web version and will make it into the PDF versions once these are updated.

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 81k

wonderdump doesn't work. I did

  1. curl http://data.biostarhandbook.com/scripts/wonderdump.sh > ~/bin/wonderdump
  2. chmod +x ~/bin/wonderdump
  3. wonderdump SRR1972739 -X 10000 --split-files

and I saw "wonderdump: no command for wonderdump."

In addition, there is no content about installing wonderdump .

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by ahramkim112810
1

Can you post the output for ls -l ~/bin/wonderdump and which wonderdump?

First two commands you have above should "install" the wonderdump script.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax74k

The outpuf of ls -l ~/bin/wonderdump is

-rwxrwxrwx 1 AR AR 1057 Jan 5 11:15 /home/AR/bin/wonderdump

Is there anything wrong?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by ahramkim112810
1

this is not the place to troubleshoot or support the code in the book. Please open a new question or send an email to the contact email.

ADD REPLYlink written 2.9 years ago by Istvan Albert ♦♦ 81k
1
gravatar for reza.jabal
2.8 years ago by
reza.jabal350
New York, USA
reza.jabal350 wrote:

Well done Istvan for this great job. It's absolutely a valuable resource for current and future students! but why not delivering a course on Coursera or edX based on this book!

ADD COMMENTlink written 2.8 years ago by reza.jabal350
2

The book us used to support an existing course offered in residence and based on student evaluation it was successful at that.

An online course based on the book is indeed a more natural and logical step - we'll see what the future holds. I am not particularly fond of the Coursera platform - I find it counterintuitive as far as the interface goes, difficult to learn with it and feels limiting in with respect of course design.

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 81k
1
gravatar for fanicesiza
2.8 years ago by
fanicesiza10
fanicesiza10 wrote:

In the Gene ontology section of this book, there is no file in the locate: http://geneontology.org/gene-associations/gene_association.goa_human.gz Please check, thanks.

ADD COMMENTlink written 2.8 years ago by fanicesiza10

Thanks for the note. It turns out that on January 8th, 2017 the Gene Ontology has changed not just the file naming but even the formats. Creating a link and results checker for the book is more urgent than ever. This will the priority this month.

I always knew that data and links are brittle in bioinformatics, but the magnitude and frequency of the problems surprised me. Just two months after the book' release and a whole bunch of links had to be changed.

The URL in question has been corrected and the examples will execute but I will need to revisit that chapter and investigate the matter a little deeper as I believe that there are more profound changes there.

By the way I also expect a whole slew of GO enrichment tools to become broken as the result of this change.

A new site for issue tracking for the book will be added soon. Details to follow.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Istvan Albert ♦♦ 81k
1
gravatar for germelcar
2.8 years ago by
germelcar20
Mexico/Ensenada/CICESE
germelcar20 wrote:

Is correct to try to cite the handbook? If yes, how would I cite it?

BWT, what about de novo transcriptome assembly? Would be great to include a section for that.

For fastq-dump, I see that the Handbook uses version 2.5.2. I remember a notice from SRA-Toolkit's github page saying that one should upgrade because of the https update on the NCBI platform. I see also that the "--split-files" option for paired-end data is used, what about "--split-3" option? I have noticed some subtle differences (and better results for using Trinity) when I use "--split-3" option instead of "--split-files" option.

Thanks in advance.

ADD COMMENTlink written 2.8 years ago by germelcar20
2

Create an "issue" for the fastq-dump question here.

ADD REPLYlink written 2.8 years ago by genomax74k

Thanks for the reply.

ADD REPLYlink written 2.8 years ago by germelcar20
1
gravatar for Lila M
2.7 years ago by
Lila M 800
UK
Lila M 800 wrote:

The book is great, but I would like to have some information related to ChIP- seq as well

ADD COMMENTlink written 2.7 years ago by Lila M 800
5

The ChIP-Seq chapter is scheduled for the end of this month (early March latest).

ADD REPLYlink written 2.7 years ago by Istvan Albert ♦♦ 81k
1

looking forward it!

ADD REPLYlink written 2.7 years ago by Lila M 800
1

I am still waiting for it! :D

ADD REPLYlink written 2.7 years ago by Lila M 800
4

It will come a bit later - hopefully this month.

We hit some issues - mostly that ChIP-Seq studies appear to be even more subjective and sensitive to parameters than initially thought. Hence we are contacting authors and trying to work with them to figure out how they got to the conclusions.

ADD REPLYlink written 2.7 years ago by Istvan Albert ♦♦ 81k
2

The ChIP-Seq chapter is now out.

ADD REPLYlink written 2.6 years ago by Istvan Albert ♦♦ 81k

I'm reading it! Thank you very much :)

ADD REPLYlink written 2.6 years ago by Lila M 800
1
gravatar for juliuspasion1994
2.7 years ago by
juliuspasion199410 wrote:

I just purchased the book, but I have Windows 7. Can anyone help me download the right programs needed to work through the book that are available on Windows 7?

ADD COMMENTlink written 2.7 years ago by juliuspasion199410
1

This thread is not the right forum for this question. Please read the first paragraph in the first post.

ADD REPLYlink written 2.7 years ago by Istvan Albert ♦♦ 81k
1
gravatar for kenanh
2.7 years ago by
kenanh10
kenanh10 wrote:

Great book!

In the section How to visualize genomic variation (What would realistic and good data look like?) it says that the script simulate-experimental-data.sh will generate a file called results.bam. It actually generates a file called align.bam.

In the section Variant effect prediction (How do I use snpEff?) the link http://data.biostarhandbook.com/variant/find-ebola-variants.sh results in a file not found error. Please check, thanks.

ADD COMMENTlink written 2.7 years ago by kenanh10
1

Please submit issues to:

https://github.com/biostars/biostar-handbook-issues/issues

In this case I have opened an issue for it:

https://github.com/biostars/biostar-handbook-issues/issues/10

Edit: the issue has been now resolved

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Istvan Albert ♦♦ 81k
1
gravatar for Istvan Albert
14 hours ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

November 1st, 2019: The Art of Bioinformatics Scripting

The Biostar Handbook has grown huge :-) it is now close to 1000 pages! To manage this complexity we have started reworking the various chapters into independent books.

Bioinformatics Data Analysis

The reorganization will allow readers to more easily locate the information that they need. It will allow us to design and formulate specific training plans that are customized to specific needs. The first book section that has been reworked covers Unix Scripting and is titled:

As always all new content is included with your subscription.

ADD COMMENTlink written 14 hours ago by Istvan Albert ♦♦ 81k
0
gravatar for mcc
2.9 years ago by
mcc80
PVD, USA
mcc80 wrote:

Has Biostar now become a sales and advertising platform for 'for-profit' books and guides?

Is Biostar the proper forum for a book, that by the sound of it, is based on the free content that is found without charge in this educational platform. Although, I applaud the efforts of the writers and editors of this book to aggregate the material for the book, I am questioning the idea of having a booklet that is a pet project for some being advertised on such an open source environment.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by mcc80
9

nah, it is not books and guides - just one book - the real deal, the Biostar Handbook. :-)

and it is not "for profit" either - it is about "loss reduction" mainly ... running this site over the past seven years has generated costs that go well over five digits ( (and in US dollars that is), or even six if you count people's time. I am thrilled to have come up with a solution that does several things at once: supports the site, imparts valuable knowledge, helps the people that need this knowledge and does that really cheap.

What you seem to complain about, that unregistered users may be shown ads a few times is a very small inconvenience.

Finally if you think that it is easy to write this book - you are welcome to try it yourself, then when done release under any licensing of your choice.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Istvan Albert ♦♦ 81k
1

Just adding my two cents here. This is an amazing book which covers a lot of material in a very smooth manner. I also love the fact that any added chapters may be seen by paying very little extra (and lectures). It certainly goes over the basics but it also covers some excellent tips for folks who are not "beginners". For the past few months I have been referring this book to several people as I truly think it will help them.

Given the amount of effort given to write the material and maintain this forum, it is needless to say that Dr. Albert has the right to add this thread about the book. And thank you Dr. Albert, for the excellent material that you shared.

ADD REPLYlink written 2.2 years ago by lshepard390

Thanks for the kind words. Much appreciated - I most pleased of the observation that the book is not just for beginners. I have made a concerted effort to have something useful to say even to those that are more experienced.

ADD REPLYlink written 2.2 years ago by Istvan Albert ♦♦ 81k
1

Um, you're welcome to continue using the site and its content gratis, so it's unclear what your beef is...

ADD REPLYlink written 2.9 years ago by harold.smith.tarheel4.5k
0
gravatar for Diego
2.8 years ago by
Diego50
Diego50 wrote:

This is amazing! Coming from software engineering, I'm pretty new to this "bio" part of bioinformatics. I'm going to buy it as soon as I can,

ADD COMMENTlink written 2.8 years ago by Diego50
0
gravatar for najibveto
2.2 years ago by
najibveto40
Korea, Republic Of
najibveto40 wrote:

thanks a lot for this amazing book and i am enjoying reading the online version. i want to know if possible to add some chapter such as :

  • study of microrna-seq in model and non model organism.
  • study of RNA-seq in non model organism.
    thanks a lot for your hard work.
ADD COMMENTlink written 2.2 years ago by najibveto40

Thank you for the kinds words - much appreciated.

A chapter on small RNA analysis would indeed be of interest to many readers and it is a section that is in the planning stages. In any case, it would be pursued after the current task of finishing the online course on the existing materials.

ADD REPLYlink written 2.2 years ago by Istvan Albert ♦♦ 81k
0
gravatar for BioBing
18 months ago by
BioBing100
Denmark
BioBing100 wrote:

I love it! Thanks for an amazing book - and the courses in bioinformatics and python!!!

When following the courses, is there a forum/thread to discuss the different lectures and topics?

ADD COMMENTlink written 18 months ago by BioBing100
1

Thanks for the kind words. I am happy to hear that the resources are effective.

You are right that we ought to have a forum of some sorts - especially since now the site hosts a book and two courses all going in parallel. We are working on addressing this shortcoming. We will likely have a forum in place this Summer - will be announced on the mailing list.

In the Fall the bioinformatics course will also likely gain a few video sections as well, similar to what the Python course has.

ADD REPLYlink written 18 months ago by Istvan Albert ♦♦ 81k

Perhaps the Biostars Slack group would be ideal for this? You could request to create a channel for the book itself and then for the lectures. It is worth a try (maybe for a test period of time).

ADD REPLYlink modified 17 months ago • written 17 months ago by lshepard390

+1 on this idea - It's a significant value addition to the Slack workspace

ADD REPLYlink written 17 months ago by RamRS24k

Thanks for book Istvan. Last year, I also bought a copy of the book with 2 years free update benefits. I was wondering if you have planned for the next update? I haven't seen any content update since Sep 2017.

ADD REPLYlink written 15 months ago by bioinfo740

There was more new content over 2017 - just a different kind - I have explored different directions this year:

  1. An online course has been added with 30 lectures finished in December 2017. I would recommend taking (and re-taking) the tests.
  2. A Python course has been started and hopefully will be finished this year.

There may be new chapters this Fall when I teach the course again - though I would expect something new there as well.

ADD REPLYlink written 15 months ago by Istvan Albert ♦♦ 81k
0
gravatar for Fanta
15 months ago by
Fanta0
Italy
Fanta0 wrote:

What are the pre-requisites to be able to use the book (and the training) for self-teaching?

ADD COMMENTlink written 15 months ago by Fanta0
3

What are the pre-requisites to be able to use the book (and the training) for self-teaching?

Intelligence.

ADD REPLYlink written 15 months ago by Istvan Albert ♦♦ 81k
3

What are the pre-requisites to be able to use the book (and the training) for self-teaching?

Willingness

ADD REPLYlink modified 15 months ago • written 15 months ago by lakhujanivijay4.5k
0
gravatar for dago
3 months ago by
dago2.5k
Germany
dago2.5k wrote:

Hi guys, the book is great! Is there any plan to extend the metagenomic part? It would be nice to include other tools and approaches for both wgs and 16S metagenome In case you can suggest other tutorials outside the book I would also be happy to go over them! Thank you!

ADD COMMENTlink written 3 months ago by dago2.5k
2

Hello dago - your suggestion to list additional learning resources after each chapter is excellent.

We will add that over the next semester.

On new chapters, it is a bit of a challenge to figure out what to cover next. PacBio, single-cell RNA-Seq and metagenomics are all appropriate subject areas. We'll see how the book evolves, we'll have new material, just not sure yet what topic ;-)

ADD REPLYlink modified 3 months ago • written 3 months ago by Istvan Albert ♦♦ 81k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1392 users visited in the last hour