Hello all,
I am putting together an ebook to describe a number of useful bioinformatics tools. The book is under development, and V0.1 is freely available at the following link.
https://leanpub.com/pandoras-toolbox
[In fact, if you grab V0.1, all updates will also be freely available to you based on leanpub rules.]
Here is what I am trying to achieve. I work with a number of biologists and they often complain about - (i) not knowing what bioinformatics tools to use for their large data files, (ii) the tools they have need more RAM etc. than what they have and (iii) not knowing how to mix/match multiple tools to do something efficiently and (iv) interpreting the results coming from various programs. For example, does Trinity giving 350,000 assembled transcripts mean the organism has 350K genes?
So, I am building together a minimal set of efficient programs to help them so that I do not need to go over the same explanation many times. The project is moving slowly, but I am making progress.
Here are some of the relevant posts -
All thoughts and suggestions are welcome.
M.
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ugly.betty77
Great initiative, and thanks for sharing. Some thoughts/suggestions:
Thank you for the great suggestions !! I agree about your comment on PHYLIP, and decided to keep it as a placeholder until finding enough time to check other options and find something better. Do you have any suggestion?
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Great job! I like the idea of having a pre-made solutions for using bioinformatics utilities. But often times, with each revision of these programs/utilities, options keep changing and your book will soon become outdated. How are going to deal with that?
If you keep the document content and resources in a Github project, you can integrate the Github repository with a readthedocs subsite through a webhook.
A
gitcommit to the project's repository can then automatically trigger re-rendering the document as HTML, as well as a PDF eBook file.We use this for updating BEDOPS documentation. We have a document made from the
docsfolder in our master branch, as well as a documentation set made for the development branch. So we can continually work on and push updates to the development branch without touching the latest stable revision. If someone has a question about a particular tool or option, I can just point them to the section's or subsection's web page directly.In addition, with this approach you gain the benefits of versioning. Say there's a typo. Or some new tool comes out, or a new version of an existing tool, which adds a useful new feature or deprecates an old one. One quick commit and your users can easily get a copy of your book with the freshest content.
Thanks Alex for the suggestion. Let me look into that.
arnstrm,
The book can be updated any time and readers can download the new version for free. So, changing options is not a problem (except it takes my time).
Moreover, the idea is to give newcomers some place to start from, not give a total package describing everything in a program. I am not trying to replace the well-maintained documentation sites by the authors of the programs.