Bioinformatics By The Bay Press

We are a publisher of print books and digital titles on bioinformatics (computational molecular biology) and related computer science topics authored by Arun Jagota, PhD in computer science and co-developer of the national award-winning bioinformatics certificate program at the University of California, Santa Cruz Extension. The published content is from the computational rather than the biological perspective.

Print books| Ebooks| ebook issues| About the author| Local| Ask a question| Learn something new | External Resources

Print books

All are at Amazon.com. Click on a link to visit a book’s Amazon page. The dates below are the publication dates.

Search Inside The Book

The entire contents of the above books (with the exception of Algorithms Q&A and Sequence Analysis Using BioSeqAnalyzer 1.0) may be searched and browsed online at Amazon.com, thanks to their wonderful ‘Search Inside The Book’ program. Click on the title links above to visit the Amazon pages of these books. From there you can launch a ‘search inside the book’. (As an added bonus, you will have experienced ‘Search Inside the Book’ if you haven’t tried it before.)

Sales Approximate Numbers

These approximate numbers are for sales at Amazon.com till July 2004. Data Analysis and Classification for Bioinformatics has sold approximately 1500 copies at Amazon.com since February 2001, Perl For Bioinformatics has sold approximately 550 copies since early 2002, Microarray Data Analysis and Visualization has sold approximately 350 copies since early 2002, and Protein Structure Informatics has sold approximately 30 copies since early 2003.

University bookstores (or others) may order these titles directly from the author/publisher. Send purchase order or inquiries to biobay@comcast.net. Other than from amazon.com, at the present time, we only accept bulk orders –  minimum quantity 10, of any mix.

Desk copies may be requested for possible use in a course. Contact biobay@comcast.net. Include your instructor and course information in your e-mail. Lecture slides are available (complimentary) for most of the books and digital matter, for instructors using or intending to use the materials in a course. Contact biobay@comcast.net to request an e-copy. Include the course information in your e-mail, and which book(s) or digital material(s) you'd like the lecture e-transparencies for.

Prosite2Perl subroutine in Perl. Courtesy of Jordan Dimov. Companion to Perl for Bioinformatics.

Local: These books are also available at DigitalGuru Bookshops, 546-3 Lawrence Expressway, Sunnyvale, CA 94085.

Ebooks

Why buy ebooks? – To permanently archive on your computer (never lose them). For easily locatable and electronically searchable reference.  Because they are priced significantly lower than equivalent print books due to lower production and distribution costs. Because they may be available on topics not yet in print or they may offer material selectively (e.g., chapters).

At ContentReserve - A wholesaler that securely distributes digital content from selected publishers to ebookstores. The titles here are offered in one or both of two formats: Microsoft Reader and Adobe ebook. The Microsoft Reader versions read surprisingly well on the screen, but are not printable, nor do math fonts come out nicely at present. The titles with significant math content are therefore offered only in Acrobat ebook format. These titles are printable (with limits) as well. The digital versions of print books are priced at 50% of the latter.

Microsoft Reader Format

Adobe ebook Reader Format

The most recent additions below are in bold.

ContentReserve Retailers

Because ContentReserve distributes to many retailers, it is a bit difficult to tell which ebookstore is carrying which of the above titles. Moreover, we have found that even when we are told that a certain ebookstore is carrying a certain title, a search does not always quickly bring it up. Here are some recommendations, based on some of our experimentation.

At eBookMall - These are direct links to some titles at this ebookstore.

ebooks: tips, cons, pros

Print books have many advantages over digital content. Having said that, over the past year or so, I have begun using digital content quite a bit as well, and have found it attractive for a number of reasons. Equivalent digital content is generally significantly lower in price than print content. Half price or less.

I like to get digital content in PDF form. I then print off a copy, and put it in a binder. Often I put related digital content in the same binder. I view this as giving me the ability to create my own "book", well sort of, which contains related material from a variety of sources. For example, if I want a "Bayes Network" collection, I will download tutorials, papers, and other materials in PDF, put them all in one binder, and then everything is in one place. In fact, there are times when I have found this to work better than a book on the same topic. Aren't there times when you like to look at the same material in more than one book in the hope that it will be presented in one of the books in a way that helps you understand it well? A binder allows you to do something like this...

When reading up on a subject in one of my binders, I also often scribble on the printed materials. At times, I will also create new sheets of notes, and simply put them in the same binder. (Of course, one could scribble on a print book as well, although one might hesitate to do so, because the scribble becomes permanent -- one can't print off a clean copy should one desire to, which you can do with your PDF. Inserting fresh pages into a book which contain one's notes would of course be quite infeasible. I do this quite a bit on binders.) Finally, a binder also has the feel (to some extent) of a hardcover book. It certainly shares the same quality of robustness that is one of the attractive benefits of hardbound books over soft-cover ones.

There are other times when I read digital content right on my laptop. For example, if I download a long PhD thesis and I do not want to read it fully, just browse it, or possibly see if it contains a specific item of interest, I will not print off a copy -- I will just put it in my library on my laptop. Reading on the laptop works well for me. Another type of item that I regularly read on my laptop is lecture notes for my classes. I find the laptop works well for "one page at a time" viewing or for searching for specific information. On the other hand, reading off printed materials is probably better when "non linear" reading may be involved, for example going back-and-forth over multiple pages. Recent developments in e-book reading technology (specifically, Microsoft Reader) may eventually lead me to do more electronic reading. At the present time, I still like my PDFs because I can both print them off and read them electronically. Microsoft reader, which is supposed to read somewhat better on the screen, does not permit printing. Another factor at the present time is that Microsoft Reader does not work well with documents containing a lot of math, while PDF is very good at them.

Here are some tips for electronic reading of PDFs to those new to PDFs. I find it very convenient to use arrow keys to flip pages. I also frequently use PDF bookmarks to go to a specific chapter or section. When all I want to do is read on my laptop, i.e., I don't wish to use other applications simultaneously, I use Ctrl+L to go into full-screen mode which I like very much. It is pretty common for me to also use the magnification icons to increase or decrease the font size (in full screen mode, use Ctrl++ to increase and Ctrl-- to decrease). There are times when I also use the search icon to search, which serves as the electronic replacement for an index at the end of a book.

About the Author

Arun Jagota teaches in the national award-winning bioinformatics certificate program at the University of California, Santa Cruz Extension, of which he is the co-developer. Click here for the descriptions of the courses. He has also co-developed a bioinformatics certificate program at the University of Alabama at Birmingham, USA, in collaboration with the chair of the computer and information sciences department.

Arun Jagota has a PhD in Computer Science from the State University of New York At Buffalo. He is presently a research scientist and part-time instructor at the University of California, Santa Cruz. He is or has been an adjunct faculty member at Santa Clara University, the University of California, Santa Cruz, at the University of Memphis, and at the University of North Texas. He has also taught at the University of California Berkeley, Extension, at the University of California, Santa Cruz, Extension, and at San Jose State University. He presently teaches a number of bioinformatics courses at UCSC extension and conducts research in bioinformatics and the related fields of neural networks and machine learning. For more information, see http://www.cse.ucsc.edu/~jagota

Local to the SF bay area

The four print books are also available at DigitalGuru Bookshops, 546-3 Lawrence Expressway, Sunnyvale, CA 94085.

I teach bioinformatics every quarter at University of California, Berkeley extension. See http://www.unex.berkeley.edu

Personal consulting

Ask technical questions by email. Questions may be statistical or computational in nature, bioinformatics or not. Send questions to biobay@comcast.net If I can't, or choose not to, answer your question, I will reply back right away. If I answer your question, I will e-mail the reply to you, and bill you for the time I spent. (Complex answers, reports, etc can be sent as PDF attachments. I have tools, including a pen and a tablet, to quickly create sketches, integrate them with text, and convert them to PDF.) My fee is $35 an hour. (I accept payments via PayPal, see http://www.paypal.com, which is very convenient for this sort of thing. A checque is fine also.) You may put a cap on the maximum amount I can charge, which should be indicated in the first email you send me. Note the simplicity of the transaction: one email from each end, followed by the payment. (The transaction can be extended over multiple rounds of questioning and answering should this be desired.)

Broad questions are welcome as well as narrow ones. Here are some examples of both types

Personalized Courses

While teaching bioinformatics courses to working professionals over a number of years I have noticed the following. Some people have had more of an interest in learning specific material and less of an interest in getting a good grade (or a certificate of having taken the class). Others have wanted to go beyond the material taught in class in specific ways. If you see yourself in the mold of a person profiled above, you might be interested in what I have to say below.

I have a keen interest in communicating interesting and useful topics in bioinformatics, data analysis, or algorithms. If you have an interest in learning some specific material on one of these topics, send me a short description of what you want by email to  biobay@comcast.net. If it interests me as well I can put together “a customized course” for you. The delivery would be over the internet in the form of email interactions, lecture notes (and maybe assignments if you’d like some) emailed as attachments, and perhaps NetMeeting for interactive presentation of complex ideas using NetMeeting’s white board and chat features. My fee is $30 per hour, or a flat course fee by mutual arrangement. (Time spent on preparing reusable lecture notes will be significantly discounted.) Here are some example courses. Your interests may be narrower or broader.

 

External Resources