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MoorhouseMBarryP: Bioinformatics Biocomputing and Perl Cherkasov, Artem Oct 12, 2004

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ralssBioMed CentBioMedical Engineering OnLineOpen AcceBook reviewReview on ''Bioinformatics, Biocomputing and Perl'' by Michael Moorhouse and Paul BarryArtem Cherkasov*Address: Division of Infectious Diseases, Faculty of Medicine, University of British Columbia. 2733, Heather street, Vancouver, British Columbia, V5Z 3J5, CanadaEmail: Artem Cherkasov* - artc@interchange.ubc.ca* Corresponding author    Book detailsMoorhouseMBarryPBioinformatics Biocomputing and PerlWiley2004506ISBN 047085331XThe book "Bioinformatics, Biocomputing and Perl" [1]attempts to encompass those numerous volumes whichmost bioinformaticians keep on their office bookshelvesand which are often entitled as "Something in a Nutshell".The book aims at both biology- and computation-ori-ented audiences and is designed as a number of 'crash-courses' quickly updating the reader on the basics of bio-informatics. It starts with a preface outlining main biolog-ical and technological concepts of the moderncomputational biology. The rest is organized into four sec-tions consisting of 18 chapters elaborating on essentialbioinformatics tools and skills.The section 'Working with Perl' presents an extended tuto-rial with practical tips and useful references for Perl begin-ners. Following this is 'Working with Data', whichfamiliarizes the reader with some public genomic andproteomic databases and discusses important subjects ofdatabase formats, non-redundancy, cross-referencing andprogrammable access, etc. By working through the section,the reader acquires basic skills for mySQL database useand DBI Perl programming.Next, the authors offer Perl-based solutions for remotedatabase access and for creation of WWW-based bioinfor-The final topic of the book, 'Working with Applications',features basic tools for sequence alignment, proteinhomology modeling and data visualization, all com-monly used in bioinformatics practice. The section alsooffers recent and relevant examples of BioPerl applica-tions.In general, the book reflects the state of bioinformaticsfield with its strengths and weaknesses. Many Perl chap-ters, such as Perl regular expressions, modular organiza-tion, DBI-programming, BioPerl and web-automation, areexcellent. The presented material is rather comprehensiveand yet easy to read – the authors spent appreciativeefforts to make the book interesting and enjoyable. Theauthors also acknowledge the open-source nature of Perland the bioinformatics community and offer on-line sup-port and direct feedback to the readers.There are also certain aspects, in which the book could befurther improved. Several sections may be too advancedfor the beginner level (such as Perl basics and databasedownloading), while others may contain too excessivedetails (the Protein Databank section). In addition, it maybe of advantage to mention AcePerl [2], Perl-programma-ble access to the SRS as well as XML- [3] and distributeddata processing by Perl. The book would greatly benefitfrom color illustrations. Several figures in the 'biological'sections are not very informative or readable (such as Fig-ure 10.5), and one contains a critical error (Figure 1.1).Published: 12 October 2004BioMedical Engineering OnLine 2004, 3:33 doi:10.1186/1475-925X-3-33Received: 07 October 2004Accepted: 12 October 2004This article is available from: http://www.biomedical-engineering-online.com/content/3/1/33© 2004 Cherkasov; licensee BioMed Central Ltd. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Page 1 of 2(page number not for citation purposes)matics services using Perl functionalities in 'Working withthe Web'.A very useful feature of the book is the use of maxims thathighlight key points throughout the text. The authors alsoPublish with BioMed Central   and  every scientist can read your work free of charge"BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime."Sir Paul Nurse, Cancer Research UKYour research papers will be:available free of charge to the entire biomedical communitypeer reviewed and published immediately upon acceptancecited in PubMed and archived on PubMed Central BioMedical Engineering OnLine 2004, 3:33 http://www.biomedical-engineering-online.com/content/3/1/33provide helpful technical comments where necessary andoffer practical exercises at the end of each chapter. Thebook is concluded with six appendices covering the Linuxbasics, Perl installation, operators, on-line support andsuggested reading materials which, in my mind, benefitthe book tremendously.Thus, the overall product, the "Bioinformatics, Biocomput-ing and Perl", serves well its purpose as an introductorytextbook and a resource of reference materials for bioin-formaticians.List of Abbreviations usedAcePerl – is a Perl interface for the AceDB – a popularobject-oriented bioinformatics database.DBI Perl – the primary interface for database program-ming by Perl.BioPerl – a collection of Perl modules specificallydesigned for several most common bioinformatics tasks.XML – Extensible Markup Language – a popular standardfor documents containing structured information.SRS – the Sequence Retrieval System – a popular rela-tional database for bioinformatics.References1. Moorhouse M, Barry P: Bioinformatics Biocomputing and Perl Wiley;2004. 2. AcePerl – for more info visit the home page of the AcePerldeveloper Dr. L. Stein at the Cold Spring Harbor Laboratory[http://stein.cshl.org/AcePerl/]3. Ray ET, McIntosh J: Perl & XML O'Reilly; 2002. yours — you keep the copyrightSubmit your manuscript here:http://www.biomedcentral.com/info/publishing_adv.aspBioMedcentralPage 2 of 2(page number not for citation purposes)


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