实验十五 Using the computer in biochemical research I. Introduction and theory The modern computer has revolutionized the way we live. Not surprisingly, the computer has also changed the way we do biochemical research. Your first encounter with a computer in this laboratory will probably be while using an instrument that has a computer to control its operation, to collect data, and to analyze data. All major pieces of scientific quipment including UV-VIS spectrometers, high-performance liquid chromatographs, gas chromatographs, nuclear magnetic resonance spectrometers, and DNA sequencers are now controlled by computers. But your use of the computer will not end in the lab. You will use a computer to prepare each laboratory report including graphical analysis of experimental data. If the computer is connected to the Internet, you will greatly broaden its use to some of the following: (1) searching the biochemical literature for pertinent books and journal articles and(2)accessing biological databases that provide nucleic acid and protein sequences and protein structures. Personal computing in biochemistry It is now possible for most students to purchase a basic computer system at low cost. Some recommendations for specific hardware and software will be given here, but one must be aware that new products and important upgrades are continually being developed For word processing( writing lab reports), basic software programs including Microsoft Word and Word Perfect are most widely used. Software specialized for scientific writing is available but probably not necessary at this level. For many experiments that you complete, you will need to present data in a spreadsheet or graphing or spreadsheet with graphing capability include Lotus, Excel, Sigmaplot, Quattropro, Kaleidagraph, and Cricket Craph. Some graphs that you prepare from experimental data will be nonlinear. The most common example is a Michaelis-Menten graph from enzyme kinetics studies(substrate concentration vS. reaction rate). Since most computers and programs have different methods for dealing with nonlinearity, it is probably best not to connect the data points with a line. Rather, use a curve-fitting routine to get the appropriate line. Alternatively, one could analyze the data using a straight-line method such as the Lineweaver-Burk plot
294 实验十五 Using the computer in biochemical research Ⅰ. Introduction and theory The modern computer has revolutionized the way we live. Not surprisingly, the computer has also changed the way we do biochemical research. Your first encounter with a computer in this laboratory will probably be while using an instrument that has a computer to control its operation, to collect data, and to analyze data. All major pieces of scientific equipment including UV-VIS spectrometers, high-performance liquid chromatographs, gas chromatographs, nuclear magnetic resonance spectrometers, and DNA sequencers are now controlled by computers. But your use of the computer will not end in the lab. You will use a computer to prepare each laboratory report including graphical analysis of experimental data. If the computer is connected to the Internet, you will greatly broaden its use to some of the following: (1) searching the biochemical literature for pertinent books and journal articles and (2) accessing biological databases that provide nucleic acid and protein sequences and protein structures. Personal computing in biochemistry It is now possible for most students to purchase a basic computer system at low cost. Some recommendations for specific hardware and software will be given here, but one must be aware that new products and important upgrades are continually being developed. For word processing(writing lab reports), basic software programs including Microsoft Word and Word Perfect are most widely used. Software specialized for scientific writing is available but probably not necessary at this level. For many experiments that you complete, you will need to present data in a spreadsheet or graphing or spreadsheet with graphing capability include Lotus, Excel, Sigmaplot, Quattropro, Kaleidagraph, and CricketCraph. Some graphs that you prepare from experimental data will be nonlinear. The most common example is a Michaelis-Menten graph from enzyme kinetics studies(substrate concentration vs. reaction rate). Since most computers and programs have different methods for dealing with nonlinearity, it is probably best not to connect the data points with a line. Rather, use a curve-fitting routine to get the appropriate line. Alternatively, one could analyze the data using a straight-line method such as the Lineweaver-Burk plot
The computer and the internet If you are using the computer as described above, you are saving time and preparing lab reports. Howe ifi cted to the Internet then you are not tapping into the vast wealth of biochemical tools and information available. The Internet can be defined, in simple terms, as a world wide matrix that allows all computers and networks to communicate with each other If the computer you are using is college owned, then it is probably already linked to the Internet. For your own home computer, you may need to subscribe to an Internet service and in a modem to transmit computer signals through a telephone line. Once you are connected to the Internet, many programs are available as freeware, software provided without charge by its creator. After you are connected to the Internet, what are the basic facilities available for use? First, you will be able to communicate by e-mail(electronic mail). Messages containing text, files, and graphics may be sent to anyone who has a computer with an Internet link and an e-mail address. Addresses have three basic components, the user name, an@ sign, and the user's location or domain. Common domains that you will encounter usually have one of the following suffixes: edu(educational institution in the United States), ac(academic institution in the United Kingdom)h, gov(government), com(commercial organization), and org(other organization). You will need an e-mail program to collect, send, and organize messages. The most popular ones are Eudora and Pegasus. (Practice your e-mail skills by sending a message, perhaps a question, to your laboratory instructor). Connected to the Internet, you will also be able to join in list server discussion groups created to share ideas in a commo area of interest or in news groups such as USENET. One of the most widely used facilities on the Internet is the ability to place and retrieve network data by file transfer protocol( ftp The World wide web The newest and most rapidly growing component of the Internet is the World wide Web(www, also called"the web"). This facility, which was launched in 1992, permits the transfer of data as pages in multimedia form consisting of text, graphs, audio, and video. The pages are linked together by hypertext pointers so that data stored on computers in different locations may be retrieved via the network by your computer Web documents are written in a special coded language called Hvper Text Markup Language(HTML). To access all of the
295 The computer and the internet If you are using the computer as described above, you are saving time and preparing good-looking lab reports. However, if your computer is not connected to the Internet, then you are not tapping into the vast wealth of biochemical tools and information available. The Internet can be defined, in simple terms, as a worldwide matrix that allows all computers and networks to communicate with each other. If the computer you are using is college owned, then it is probably already linked to the Internet. For your own home computer, you may need to subscribe to an Internet service and obtain a modem to transmit computer signals through a telephone line. Once you are connected to the Internet, many programs are available as freeware, software provided without charge by its creator. After you are connected to the Internet, what are the basic facilities available for use? First, you will be able to communicate by e-mail(electronic mail). Messages containing text, files, and graphics may be sent to anyone who has a computer with an Internet link and an e-mail address. Addresses have three basic components, the user name, an @ sign, and the user’s location or domain. Common domains that you will encounter usually have one of the following suffixes: edu(educational institution in the United States), ac(academic institution in the United Kingdom), gov(government), com(commercial organization), and org(other organization). You will need an e-mail program to collect, send, and organize messages. The most popular ones are Eudora and Pegasus. (Practice your e-mail skills by sending a message, perhaps a question, to your laboratory instructor). Connected to the Internet, you will also be able to join in list server discussion groups created to share ideas in a common area of interest or in news groups such as USENET. One of the most widely used facilities on the Internet is the ability to place and retrieve network data by file transfer protocol(ftp). The World Wide Web The newest and most rapidly growing component of the Internet is the World Wide Web(WWW, also called “the web”). This facility, which was launched in 1992, permits the transfer of data as pages in multimedia form consisting of text, graphs, audio, and video. The pages are linked together by hypertext pointers so that data stored on computers in different locations may be retrieved via the network by your computer. Web documents are written in a special coded language called HyperText Markup Language(HTML). To access all of the
resources on the Web, you will need a browser an interface program that reads hypertext and displays Web pages on your computer. The most commonly used Web browsers are Internet Explorer and Netscape Navigator. To access the Web, the Web browser is activated. Displayed on the screen will be the home page or starting point for entry into the Web. On this page will be a dialogue box into hich you can type text. The dialogue box may ask for“ Address”,“ Netsite”,“ Location”,or "URL"(Uniform Resource Locator), To request a specific Web page from another computer sitetypeintheWebpageaddresswhichisusuallyintheformhttp:/www..thEhomepage with instructions on the use of the Web site, will then be displayed on the screen. One important feature you will note is that some words on the page are highlighted. If you click the mouse on one of these words(called hyperlinks) your computer will connect to another related, Web page that provides information on the hyperlink. This feature greatly enhances the use of the Web because related Web sites are connected or linked together and may be quickly accessed by a click of the mouse. Web addresses that useful for biochemical research are presented in Tables ElI and El. 2. Many of the current Web sites you will need are listed here; however, what about new sites are created every year. To access these new sites, you need the help of a search engine, a searchable directory that organizes Web pages by subject classification. Major search engines include Alta Vista, Excite, HotBot, Lycos, Netscape Search, and Yahoo As you"surf the Web", you may find sites you wish to save and review at a later date. You may use the “ bookmark”( Netscape)or“ favorite”( Explorer) function to save it for the future Application of the Web It is not necessary to have a complete understanding of the Internet in order to ta vast resources. The fundamental concepts provided here will allow you to take advantage of two essential activities: (1)biochemical literature searching and (2)using Web directories and biological databases. The biochemical literature Experimental biochemists do not spend all their working time in the laboratory. An important component of a biochemistry research project is a search of the biochemical literature. The library should be considered a tool for experimental biochemistry in the same ay as any scientific instrument
296 resources on the Web, you will need a browser, an interface program that reads hypertext and displays Web pages on your computer. The most commonly used Web browsers are Internet Explorer and Netscape Navigator. To access the Web, the Web browser is activated. Displayed on the screen will be the home page or starting point for entry into the Web. On this page will be a dialogue box into which you can type text. The dialogue box may ask for “Address”, “Netsite”, “Location”, or “URL”(Uniform Resource Locator). To request a specific Web page from another computer site, type in the Web page address, which is usually in the form http://www.-. The home page, with instructions on the use of the Web site, will then be displayed on the screen. One important feature you will note is that some words on the page are highlighted. If you click the mouse on one of these words(called hyperlinks) your computer will connect to another, related, Web page that provides information on the hyperlink. This feature greatly enhances the use of the Web because related Web sites are connected or linked together and may be quickly accessed by a click of the mouse. Web addresses that useful for biochemical research are presented in Tables E1.1 and E1.2. Many of the current Web sites you will need are listed here; however, what about new Web sites that have been established since publication of this book? Millions of new Web sites are created every year. To access these new sites, you need the help of a search engine, a searchable directory that organizes Web pages by subject classification. Major search engines include AltaVista, Excite, HotBot, Lycos, Netscape Search, and Yahoo! As you “surf the Web”, you may find sites you wish to save and review at a later date. You may use the “bookmark”(Netscape) or “favorite”(Explorer) function to save it for the future. Application of the Web It is not necessary to have a complete understanding of the Internet in order to tap into its vast resources. The fundamental concepts provided here will allow you to take advantage of two essential activities: (1) biochemical literature searching and (2) using Web directories and biological databases. The biochemical literature Experimental biochemists do not spend all their working time in the laboratory. An important component of a biochemistry research project is a search of the biochemical literature. The library should be considered a tool for experimental biochemistry in the same way as any scientific instrument
Table el.1 Web database directories URL Pedro’s Biomolecularhttp://www.public.iastate.edu/-pedro/research-tools.html Biology workbench http://biologv.ncsauiuc.edu CmsMolecularBiologyhttp://www.sdsc.edu/restools/cmshp.html Resources BioTech http://biotech.icmb.utexas.edu Protocol Online http://www.protocol-online.net Chem connection httpichEmconnect.com/news/iournals.html AmericanChemicalSocietyhttp://pubs.acs.orgl Table el. 2 biochemical Databases and tools Name Description URL ProteinDataBank(pdb)Proteinstructureshttp://www.rcsb.org/pdbl determined by X-ray and NMr European Bioinformatics DNA sequences http://www.ebi.ac.uk/ Institute(EBi) Center forvarietyofdatabaseshttp://www.nlm.nihgov/ Biotechnology and resourees Information(NCBI) wISS-Proteln Proteinsequenceshttp://www.expasy.ch/tools/ and analysis Biocatalysis/Biodegradation Microbial http://www.labmed.umnedu Databases of the University metabolism of many umbbd/index. html of minnesota chemicals RebaSe-thERestrictionrestrictionenzymehttp://rebase.neb.com/ Enzyme Database directory and action GeorgiainStituteofTutorialsonpdBhttp://www.chemistry.gatech.edw/ Technology and Ras Mol faculty/williams/b Course information/4582/labs/rasmol- db. html
297 Table E1.1 Web Database Directories Name URL Pedro’s Biomolecular Research Tools http://www.public.iastate.edu/~pedro/research-tools.html Biology Workbench http://biology.ncsa.uiuc.edu CMS Molecular Biology Resources http://www.sdsc.edu/ResTools/cmshp.html BioTech http://biotech.icmb.utexas.edu Protocol Online http://www.protocol-online.net Chem Connection http://chemconnect.com/news/journals.html American Chemical Society http://pubs.acs.org/ Table E1.2 Biochemical Databases and Tools Name Description URL Protein Data Bank(PDB) Protein structures determined by X-ray and NMR http://www.rcsb.org/pdb/ European Bioinformatics Institute(EBI) DNA sequences http://www.ebi.ac.uk/ National Center for Biotechnology Information(NCBI) Variety of databases and resources http://www.nlm.nih.gov/ Swiss-Protein Protein sequences and analysis http://www.expasy.ch/tools/ Biocatalysis/Biodegradation Databases of the University of Minnesota Microbial metabolism of many chemicals http://www.labmed.umn.edu/ umbbd/index.html REBASE-The Restriction Enzyme Database Restriction enzyme directory and action http://rebase.neb.com/ Georgia Institute of Technology Tutorials on PDB and RasMol http://www.chemistry.gatech.edu/ faculty/Williams/bCourseinformation/4582/labs/rasmolpdb.html
TheInstituteforGenomicCollectionofgenomichttp://www.tigr.org Research RasMol( Rasmac) Moleculargraphicshttp://www.umass.edu/ for proteins microbio/rasmol Predict Protein Proteinsequenceandhttp://www.embl-heidelberg.de/ structure prediction predictprotein/ Gene quiz Proteinfunctionhttp://www.sander.ebi.dc.uk/ analysis based on gqsrv/submit equence The use of the biochemical literature by the student in biochemistry laboratory is not as extensive as that of a full-time researcher, but you must be aware of what is available in the library and how to use it The library is used in all stages of research. Before an investigator can begin experimentation, a research idea must be generated. This idea develops only after extensive reading and study of the literature. A research project usually begins in the form of a question to be answered or problem to be solved. For ease of solution, a major project is subdivided into questions that may be answered by experimentation Before laboratory work can begin, the researcher must have a knowledge of the past and current literature dealing with the research area. This can be reduced to two questions: What is the current state of knowledge in the area? And what are the significant unknowns? These questions can be answered only by developing a familiarity with the biochemical literature. The researcher will find that this knowledge of the literature is also invaluable for the design of experiments. The development of experiments requires knowledge of techniques and laboratory procedures. Excellent methods books and journals are available that provide experimenta details. Finally, while performing experiments, the researcher often needs physical and hemical constants and miscellaneous information. Various handbooks and encyclopedias are excellent for this purpose. The beginning student in biochemistry laboratory will not be expected to proceed through all of these stages in the design of an experiment. However, a familiarity with the literature will increase your understanding of the experiment and may aid in the development of more effective methods. When you do begin a research program, you will be able to use the library to the fullest advantage. The biochemical literature is massive and expanding rapidly. It is almost a full-time job just to maintain a current awareness of a specialized research area. There are few disciplinary boundaries in the study of biochemistry. The biochemical literature overlaps into the biological sciences, the physical sciences, and the basic medical sciences The intent of the following discussion is to bring some order to the many textbooks, reference books, 298
298 The Institute for Genomic Research Collection of genomic databases http://www.tigr.org/ RasMol(RasMac) Molecular graphics for proteins http://www.umass.edu/ microbio/rasmol/ Predict Protein Protein sequence and structure prediction http://www.embl-heidelberg.de/ predictprotein/ Gene Quiz Protein function analysis based on sequence http://www.sander.ebi.dc.uk/ gqsrv/submit The use of the biochemical literature by the student in biochemistry laboratory is not as extensive as that of a full-time researcher, but you must be aware of what is available in the library and how to use it. The library is used in all stages of research. Before an investigator can begin experimentation, a research idea must be generated. This idea develops only after extensive reading and study of the literature. A research project usually begins in the form of a question to be answered or problem to be solved. For ease of solution, a major project is subdivided into questions that may be answered by experimentation. Before laboratory work can begin, the researcher must have a knowledge of the past and current literature dealing with the research area. This can be reduced to two questions: What is the current state of knowledge in the area? And what are the significant unknowns? These questions can be answered only by developing a familiarity with the biochemical literature. The researcher will find that this knowledge of the literature is also invaluable for the design of experiments. The development of experiments requires knowledge of techniques and laboratory procedures. Excellent methods books and journals are available that provide experimental details. Finally, while performing experiments, the researcher often needs physical and chemical constants and miscellaneous information. Various handbooks and encyclopedias are excellent for this purpose. The beginning student in biochemistry laboratory will not be expected to proceed through all of these stages in the design of an experiment. However, a familiarity with the literature will increase your understanding of the experiment and may aid in the development of more effective methods. When you do begin a research program, you will be able to use the library to the fullest advantage. The biochemical literature is massive and expanding rapidly. It is almost a full-time job just to maintain a current awareness of a specialized research area. There are few disciplinary boundaries in the study of biochemistry. The biochemical literature overlaps into the biological sciences, the physical sciences, and the basic medical sciences The intent of the following discussion is to bring some order to the many textbooks, reference books