- Email: [email protected]
Zoology www guide
ARTICLE IN PRESS
ZOOLOGY Zoology 108 (2005) 179–180 www.elsevier.de/zool
SHORT COMMUNICATION
Zoology www guide Georg Hemmrich
Today nearly every Zoologist is confronted with a continously growing flow of data from various databanks, virtual libraries and other online resources. Thus, evaluation of whether these data are useful and/or significant is getting more and more difficult. The following websites give helpful examples and advice of accessing, examining and interpreting biological data. Readers are welcome to send website suggestions for future editions of Zoology to tbosch@zoologie. uni-kiel.de
The BIOSIS Biology Browser Trying to answer a biological question or finding a suitable online resource in the Internet using common search engines often leads to a flood of unwanted or unfitting results. In the last 5 years more and more people face this problem and try to invent searcheable databases which gather biological information. A crucial point in the creation process of such a database is the way how the end-user will come to grips with it. A nice example for a good structured and easy accessible online resource is the Biology Browser from THOMSON BIOSIS at www.biologybrowser.org (Fig. 1). This website gathers information about research data, online literature, biological specimen and digital instruments like biological software and online tools. In addition it provides a nomenclature glossary for Zoology and a zoological record thesaurus. The authors of the website also found a nice way to search information to a certain topic. Queries can be made in categories like Organisms, Subjects or Geography which focuses a search from the beginning. For those who want to stay up to date about E-mail address: [email protected] (G. Hemmrich). 0944-2006/$ - see front matter r 2005 Elsevier GmbH. All rights reserved. doi:10.1016/j.zool.2005.04.001
the data stored, the website also provides a newsletter service.
2Can – Bioinformatics for everyone This website is provided by the European Bioinformatics Institute (EBI) and gives beginners but also yet experienced users an insight into what bioinformatics is and how to use online tools at EBI and other webservers. From www.ebi.ac.uk/2can (Fig. 2) the user can directly follow the 2Can link and is led to a comprehensive and elaborate ‘‘who is who’’ and ‘‘what is what’’ in bioinformatics. Beside general informations about EBI one gets an introduction into various aspects of bioinformatics and biological databases. Also included is a list of helpful tutorials which help the bioinformatics-beginner to use tools like Blast, Fasta, ClustalW or a genome browser. The more experienced users can learn how a Blast-search really functions or how to use the sequence retrieval system SRS to get sequence data from a database. The 2can Educational resource can and should be used by a wide range of people from undergraduate student to senior scientist.
Tutorial – How to draw a phylogenetic tree? This website may be of particular interest for all those zoologists who use sequence data to get information about phylogenetic relationships. The Institute for computational biomedicine ICB at the Weill Medical College of Cornell University gives on their education website http://icb.med.cornell.edu/education/courses/ introtobio/t-phylogeny.xml (Fig. 3) a comprehensive introduction into phylogenetic evaluation of sequence
ARTICLE IN PRESS 180
G. Hemmrich / Zoology 108 (2005) 179–180
Fig. 1. BIOSIS – biology browser.
Fig. 3. Tutorial – Phylogenetic tree.
two phylogenetic-tree construction programs by detailed tutorials with additional example data sets. For those who are not familiar with the subject, premises like sequence retrieval, homology searching and multiple sequence alignments are explained in separate tutorials.
Fig. 2. 2Can at EBI.
data. This site provides information about phylogenetic terminology and methods how phylogeny can be examined. The reader is introduced into the usage of
ZOOLOGY Zoology 108 (2005) 179–180 www.elsevier.de/zool
SHORT COMMUNICATION
Zoology www guide Georg Hemmrich
Today nearly every Zoologist is confronted with a continously growing flow of data from various databanks, virtual libraries and other online resources. Thus, evaluation of whether these data are useful and/or significant is getting more and more difficult. The following websites give helpful examples and advice of accessing, examining and interpreting biological data. Readers are welcome to send website suggestions for future editions of Zoology to tbosch@zoologie. uni-kiel.de
The BIOSIS Biology Browser Trying to answer a biological question or finding a suitable online resource in the Internet using common search engines often leads to a flood of unwanted or unfitting results. In the last 5 years more and more people face this problem and try to invent searcheable databases which gather biological information. A crucial point in the creation process of such a database is the way how the end-user will come to grips with it. A nice example for a good structured and easy accessible online resource is the Biology Browser from THOMSON BIOSIS at www.biologybrowser.org (Fig. 1). This website gathers information about research data, online literature, biological specimen and digital instruments like biological software and online tools. In addition it provides a nomenclature glossary for Zoology and a zoological record thesaurus. The authors of the website also found a nice way to search information to a certain topic. Queries can be made in categories like Organisms, Subjects or Geography which focuses a search from the beginning. For those who want to stay up to date about E-mail address: [email protected] (G. Hemmrich). 0944-2006/$ - see front matter r 2005 Elsevier GmbH. All rights reserved. doi:10.1016/j.zool.2005.04.001
the data stored, the website also provides a newsletter service.
2Can – Bioinformatics for everyone This website is provided by the European Bioinformatics Institute (EBI) and gives beginners but also yet experienced users an insight into what bioinformatics is and how to use online tools at EBI and other webservers. From www.ebi.ac.uk/2can (Fig. 2) the user can directly follow the 2Can link and is led to a comprehensive and elaborate ‘‘who is who’’ and ‘‘what is what’’ in bioinformatics. Beside general informations about EBI one gets an introduction into various aspects of bioinformatics and biological databases. Also included is a list of helpful tutorials which help the bioinformatics-beginner to use tools like Blast, Fasta, ClustalW or a genome browser. The more experienced users can learn how a Blast-search really functions or how to use the sequence retrieval system SRS to get sequence data from a database. The 2can Educational resource can and should be used by a wide range of people from undergraduate student to senior scientist.
Tutorial – How to draw a phylogenetic tree? This website may be of particular interest for all those zoologists who use sequence data to get information about phylogenetic relationships. The Institute for computational biomedicine ICB at the Weill Medical College of Cornell University gives on their education website http://icb.med.cornell.edu/education/courses/ introtobio/t-phylogeny.xml (Fig. 3) a comprehensive introduction into phylogenetic evaluation of sequence
ARTICLE IN PRESS 180
G. Hemmrich / Zoology 108 (2005) 179–180
Fig. 1. BIOSIS – biology browser.
Fig. 3. Tutorial – Phylogenetic tree.
two phylogenetic-tree construction programs by detailed tutorials with additional example data sets. For those who are not familiar with the subject, premises like sequence retrieval, homology searching and multiple sequence alignments are explained in separate tutorials.
Fig. 2. 2Can at EBI.
data. This site provides information about phylogenetic terminology and methods how phylogeny can be examined. The reader is introduced into the usage of