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Review by Trends in Genetics 1996 The rapid growth in the number of on-line information and analysis resources available to biologists using the Internet, especially via the World Wide Web (WWW), has been astonishing. This growth is primarily the result of two factors:
1) setting-up a WWW site is fairly easy, and 2) providing a site for other researchers to use is a good way to publicize one's work to a world-wide audience. For biological database and software developers, setting-up a web site allows anyone in the world with any type of computer an Internet connection to run and use your tools. For users, the challenge is finding and learning how to effectively exploit these often extremely useful on-line resources. The latter is the issue addressed by the book reviewed here.
Internet for the Molecular Biologist is a collection of chapters contributed by a number of authors and covers a broad range of net-related topics. The first six chapters, all by G. Findlay, provide a general introduction to the Internet, briefly covering its history, types of services available (such as email, Usenet news, Gopher and WWW), how to get connected, and how to publish on the Internet. The seventh chapter, by T.S. Pillay, gives a fairly detailed account of how to retrieve sequence reports from, and how to submit searches to, a large number of available electronic mail servers, such as those maintained by the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI). This chapter is largely superfluous since the easiest method to access these servers is either through automated front-end utilities, such as the Mail Server Utility program (see http://www.ebi.ac.uk/biocat/e-mail_Server_tools.html), or directly through the WWW front-ends to these servers (e.g., see the ABIM metasite). The eighth chapter, contributed by J.W. Fickett and R. Guigo, provides extremely useful descriptions of the use of the currently available gene and gene-feature identification tools (such as the BCM GeneFinder, GeneID and Grail). This chapter is a good model for the type of site /tool review format that would be most beneficial to new users of on-line resources. The ninth and tenth chapters, describing the use of the
BIOSCI/BIONET Email Server (by D. Kristofferson) and the BioMoo (by G. Glusman, E. Mercer, and I. Rubin), respectively, will be of limited value to most readers. The bionet newsgroups provide an important channel of communications among biologists, but this chapter provides little practical knowledge, especially for the majority of users who directly access these newsgroups using Netscape or a dedicated Usenet newsreader, rather than via email. The BioMoo provides a text-based communications environment that can be used simultaneously by multiple users to conduct real-time world-wide group sessions, seminars, and courses. However, the awkwardness of using a purely text-based system, compared, for example, to a full audio and video teleconferencing system, has limited its acceptance in the scientific community.
The last five chapters are compendiums of on-line resources with short descriptions. These chapters cover Internet resources for 1) human and mouse molecular genetics, 2) fungi, 3) invertebrates, 4) plant molecular biology, and 5) microbiology. Because of their narrower range and because each chapter was contributed by researchers working in these respective areas, these chapters generally provide more in depth coverage than the corresponding areas in Smagula book. The editors have constructed a web page so that readers can directly access these resources: While the book will be useful to Internet novices, finding a computer-savvy colleague in one's department or institution who is willing to show you the ropes is generally the best way for a totally naive user to learn how to both get connected to the Internet and how to effectively use on-line resources as a research tool.
Biological Abstracts/RRM 48 (8): 131999. August 1996
The Biochemist: October/November 1996 The basics of the Internet-from e-mail messages, databases, newsgroups and the World Wide Web-are discussed and explained in easy-to-follow sections with both further reading and pointers to on-line documentation. Advanced functions, such as sequence retrieval and database screening, are covered in great detail with step-by-step examples and full explanations of all commands and results. The sections covering specific resources for human and mouse genetics, fungi, invertebrates, plants and microbes provide an invaluable reference library and should prove to be well worth investigating.
I feel that this book is not only value for money as a tutorial, but essential as a guide to locating other Internet resources. I spent an enjoyable day reading the book and the next three days following up and further investigating the resources. This is a reference I will be consulting time and time again.
Heredity 77 (1996) 448-451 The Genetical Society of Great Britain With the internet being the darling of the media nowadays a plethora of dubious titles claiming to instruct the general populace on the joys of the internet abound. Thus it was with some trepidation that I approached this book. What should a volume claiming to be for the molecular biologist do? It must inform the newcomer as to what the internet does and how to get on it. Having excited the novice the book then needs to act as a reference to some of the more important sites on the internet. In these two areas the book certainly succeeds. The book effectively splits itself into two parts, one giving information on the internet and what types of service are available and the second a reference section detailing important internet sites.
The introductory chapters explain what the internet is and its rather bizarre nomenclature. The authors are realistic; they inform the reader enough to remove the mystery, while recognising that techno-babble can turn users off. The different types of access to the internet are covered, e.g. e-mail, WWW and gopher. The detail given is enough to allow the user to either access the services themselves (e.g. mailing lists) or to go to their network manager armed with knowledge of what they require. For many users the ability to explain what they want to their computing colleagues may well justify the purchase of the book.
Once connected the next two chapters take the reader through some of the remote software tools available for sequence retrieval and analysis and computational gene identification. Anyone who has not used a remote analysis system will find this an enormous boon. To use these programs the user e-mails a request (usually containing a sequence) to the server which merrily does its magic and e-mails the results. This means that even if the only networking available is email the most powerful machines around the world can be accessed. In fact an incredible amount of the real work of the internet is done in just this way. Several different servers and the programs they run are detailed along with how to get help on them. This is important because in a small book it is not possible to detail all the options available. Rather like a large-scale map marked with the tourist information offices, this book gives a good guide to how to get there and where to go to get more detail.
The final five chapters are pure reference, consisting of listings of internet resources for human and mouse (27 pages), fungi (6 pages), invertebrates (6 pages), plants (6 pages) and microbiology (7 pages). Obviously World Wide Web sites predominate but all the major FTP sites, news groups and servers are covered. For those who already are connected these five chapters are the justification for buying the book. The coverage is sufficient to ensure that they remain useful for some time. I heartily recommend this volume for anyone who uses or wishes to use the internet.
...a guide that aims to help the 'computer illiterate' scientist get motoring on the 'superhighway' is timely....there are some really good parts to this book....a clearly written introduction to the mysteries of Email, mailing lists, newsgroups and other Internet tools....the chapter by Glusman et al. on how to meet other biologists in a BioMOO virtual world made me want to have a go!....the highlight of the book is the chapter by Fickett and Guigo on 'Computational Gene Identification'....excellent guide to gene identification....this book would have been excellent if it had been half the length...
Examples of how the Internet is used by molecular biologists were informative...useful for those who have just linked to the Internet.
Randall F. SmithBioinformatics Research Group, SmithKline Beecham Pharmaceuticals R&D, UW2230, 709 Swedeland Rd, PO Box 1539, King of Prussia, PA 19406 USA.
(http:/
/www.ccc.nottingham.ac.uk/~mbzsrs/IFTMB.HTML).
Review by
BIOSIS 2100 Arch Street, Philadelphia, PA 19103-1399 USA
This book is intended as a guide to the Internet for molecular biologists who are not computer literate. The work covers all aspects of the Internet from elementary to advanced. Topics covered include the history and governance of the Net, the principles of machine addressing, the means by which information is distributed across the Internet, (including file transfer methods and ways of connecting), types of software pointers, (including Web browsers), publishing and communication with the Net, biological newsgroups, real-time communication, and Internet sources for biology. The work has a World Wide Web page. A glossary and an index are provided.
Review by
DAVID CAINE Lark Technologies Inc., Hove, UK
In the last few years the Internet has grown to the point that it now impacts on almost all walks of life in a major way. In many respects an e-mail address has become as important a communication facility as a fax machine or even telephone. The Internet has also developed into a major tool for scientists, and in particular molecular biologists, offering the ability to screen databases, analyse sequences for functional motifs and swap research tips with other researchers. The Internet is becoming as important as some laboratory techniques in aiding research. There is no need to be a computer boffin to start benefiting from the wealth of information available since many of the programs and facilities explored in the book have very user-friendly interfaces.
Review by
Michael RhodesUK HGMP Resource Centre, Hinxton Hall, Hinxton, Cambridge, CB10 lRQ, UK.
Review from
Trends in Biochemical Sciences
Review from
Society for General Microbiology, Quarterly