Book Description

Informatics in the genomic setting involves the storage, search, and manipulation of textual data such as DNA and protein sequences and related matter such as structural or functional annotations, authors, cross-links to other sequences or structures, and more. (See the Genbank, EMBL, and PDB databases to get a better idea.) While some of the search and manipulation needs of a user may be met by generic web interfaces, often they won't be.Some needs may not have been anticipated when the web interface was constructed, others perhaps were too complex to support for use over the web.

Perl is an ideal language for such needs. With Perl one will sometimes be able to solve a data search or manipulation problem in a matter of hours if not minutes. (Solving the same problem in C/C++/Java could take much, much longer.)Here are some particular problems in this setting for which Perl is a great fit.

 Searching sequence databases with regular expression patterns.

 Parsing entries in databases (e.g., reading a Genbank entry of a gene and extracting its exons).

 Converting database entries from one format to another (e.g., converting from Genbank to EMBL format).

 Using standard sequence analysis tools written in Perl. (See the various Perl packages supported by the BioPerl project.)

This short book introduces Perl to the bio or computer scientist interested in or working in bioinformatics. Chapter 1 covers data types. Chapter 2 covers control structures.Chapter 3 covers input and output. Chapter 4 covers regular expressions. Chapter 5 covers handy functions on strings. Chapter 6 covers subroutines. All these chapters contain illustrative examples from bioinformatics. These chapters cover only those features of Perl that are particularly important to know in the context of search and manipulation of biomolecular data. In particular, Unix-specific features such as those involving Unix file, directory and process management are omitted. Chapter 7 presents several Perl scripts for various common bioinformatics tasks. Chapter 8 covers the BioPerl project.

Chapter 9 presents some modules, with examples from bioinformatics. ... Read more

Reviews (4)

What can Perl be used for in bioinformatics?
This is a brief introduction to some of the things that one can do in Perl; it lacks scope and has few useful examples, but gives a flavor for what is available. It needs some programming experience to get much out of it.

At best, an extremely pricey handbook
Although the editorial review claims that Perl for Bioinformatics "introduces Perl to the bio/computer scientist interested in or working in bioinformatics," this is really a bit of a misnomer. While it does contain a decent quantity of useful, relevant reference information for a bioinformatics student, the (dollar) price tag is far too high. Furthermore, no real introduction to Perl is found in the book, save the preface in pp. 4-5--that is to say, some basic knowledge of Perl will be an absolute requirement. As a student, I would personally lean toward any of the excellent O'Reilly bioinformatics and/or Perl books myself; they are well written, contain much of the same relevant information with additional explanations, and at a much lower price per page. Bottom line: You may find Perl for Bioinformatics useful as a pocket reference guide, but it is probably not worth the astronomical price.

too short to be really useful
Look at other general intro books on Perl, and ask yourself: how much useful stuff can any human cram into a 43-page book for beginners? The answer is: not much. I see very little sense in investing in this tiny book.

The book for the programming in bioinformatics...
If you are computer scince reseacher and very interested in BioInformation or Computational Biology, you can get very much useful things from this book. ... Read more

Book Description

 

Solving modern biological problems requires advanced informatics and computational methods. Key techniques include database management, data modeling, pattern recognition, data mining, query processing and visualization of biological data. Until very recently, virtually all public databases were simply large flat files stored in simple format. Navigating among databases required expert knowledge and considerable patience. The huge quantities of biological data and escalating demands of modern biological research increasingly require the sophistication and power of information technology tools. More specifically, optimal use of these tools requires proximity information ? knowing which data points are in the surrounding area of others.

In this book we will present methodologies and data structures for gathering high-quality approximations of biological information, and will use these information technologies as the foundation to develop practical tools for clustering and visualization in biological data mining and database management.

Book Description

Informatics in the genomic setting involves the storage, search, and manipulation of textual data such as nucleotide and protein sequences and related matter such as structural or functional annotations, authors, cross-links to other sequences or structures, and more. (See the Genbank, EMBL, and PDB databases to get a better idea.) While some of the search and manipulation needs of a user may be met by generic web interfaces, often they won't be.Some needs may not have been anticipated when the web interface was constructed, others perhaps were too complex to support for use over the web.

Perl is an ideal language for such needs. With Perl one will sometimes be able to solve a data search or manipulation problem in a matter of hours if not minutes. (Solving the same problem in C/C++/Java could take much, much longer.)Here are some particular problems in this setting for which Perl is a great fit.

- Searching sequence databases with regular expression patterns.
- Parsing entries in databases (e.g., reading a Genbank entry of a gene and extracting its exons).
- Converting database entries from one format to another (e.g., converting from Genbank to EMBL format).
- Using standard sequence analysis tools written in Perl. (See the various Perl packages supported by the BioPerl project.)

(For the second edition: As it turns out, Perl is a great language also for rapid development of various sophisticated algorithms used in bioinformatics, especially those in sequence analysis. This can be useful for students in a course who quickly want to implement such algorithms and do 'real' things with them. It can also be good in a scientific or professional setting where biologists want certain questions answered, and their computer colleagues can quickly put together Perl scripts to do what they want. )

This short book introduces Perl to the bio or computer scientist who is interested in or working in bioinformatics. Chapter 1 covers data types. Chapter 2 covers control structures.Chapter 3 covers input and output. Chapter 4 covers regular expressions. Chapter 5 covers handy functions on strings. All these chapters contain illustrative examples from bioinformatics. These chapters cover only those features of Perl that are particularly important to know in the context of search and manipulation of biomolecular data. In particular, Unix-specific features such as those involving Unix file, directory and process management are omitted. Chapter 6 touches on subroutines. Chapter 7 presents several Perl scripts for various common bioinformatics tasks (there are some additions in the second edition). Chapter 8 - a relatively big new chapter added in the second edition - describes several bioinformatics algorithms such as those used in fragment assembly, heuristic local alignment, automated motif discovery, classification of sequences, optimal sequence-to-sequence alignment, optimal sequence-to-profile alignment, heuristic multiple alignment, profile hidden Markov models, and phylogenetic analysis and presents Perl scripts for them. Chapter 9 covers the BioPerl project. Chapter 10 covers some Perl modules of use in bioinformatics. ... Read more

Book Description

This book constitutes the refereed proceedings of the Second Symposium on Intelligence and Security Informatics, ISI 2004, held in Tucson, AZ, USA in June 2004. The 29 revised full papers and 12 revised short papers presented together with 6 extended abstracts of posters and 3 panel discussion summaries were carefully reviewed and selected for inclusion in the book. The papers are organized in topical sections on bioterrorism and disease informatics; data access, privacy, and trust management; data management and mining; deception detection; information assurance and infrastructure protection; monitoring and surveillance; security policies and evaluation; and social network analysis. ... Read more

Book Description

"The Brain- From Fuzzy Arithmetic to Quantum Computing" presents an original and astounding new understanding of the brain by taking into account novel achievements in Fuzziness and Quantum Information Theory. Bringing together Neuroscience, Soft Computing, Quantum Theory, and recent developments in mathematics the actual knowledge about the brain functioning is formalized into a coherent theoretical framework. This monograph develops new and powerful neural models providing formal descriptions of biochemical transactions in the brain to guide neuroscience experiments and to better interpret their results. This book demonstrates how the physiology of the neuron can be understood based on the fundamentals of fuzzy formal languages and introduces the basics of quantum computation and quantum information to the brain. ... Read more

Book Description

The four-volume set LNCS 3480-3483 constitutes the refereed proceedings of the International Conference on Computational Science and Its Applications, ICCSA 2005, held in Singapore in May 2005. The four volumes present a total of 540 papers selected from around 2700 submissions. The papers span the whole range of computational science, comprising advanced applications in virtually all sciences making use of computational techniques as well as foundations, techniques, and methodologies from computer science and mathematics, such as high performance computing and communication, networking, optimization, information systems and technologies, scientific visualization, graphics, image processing, data analysis, simulation and modelling, software systems, algorithms, security, multimedia etc. ... Read more

Book Description

This book constitutes the refereed proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2005, held in Cambridge, MA, USA in May 2005. The 39 revised full papers presented together with abstracts of keynote talks were carefully reviewed and selected from 217 submissions. As the top conference in computational molecular conference, RECOMB addresses all current issues in algorithmic and theoretical bioinformatics. ... Read more