Computers are able to accomplish a sequence analysis, and they could easily search databases for sequences without any problem had not the dimensions of the databases also increased to an equal degree. The number of the computers and programs in the laboratories has increased a lot, but the number of specialists has not, and each one must carry out his or her own work. Today almost everything can be done through computer. In regular routine, the computer is used most frequently for word processing. Every day, people must write letters, plan production schedules, and so on. Occasionally, papers must be written. Publishing is to the successful scientist as water is to a dehydrated soup.
Regardless of what Microsoft says, word processing programs such as Word are conceived for writing letters and smaller papers, not for diplomas or for doctoral theses. Although these programs offer all kinds of comfort, such as automatic numbering and colorful graphics, longer texts that takefull advantage of all of the possibilities of the program usually have increasing problems, and you may experience a total collapse, most likely when the work is practically perfect. You can chop upthe text into smaller segments of approximately 50 pages as a precaution, or you can purchase a professional layout program.
For many, the second most important use of the computer is email (electronic mail ). With email, you can keep a collaboration alive, arrange to meet people, discuss live with specialists sitting even in some other country and so on.
There is also the Internet. Presumably, every child is aware of this concept. It is the world of colorful pictures and web sites that can be surfed. The Internet earns the commendation “of utmost value to the researcher,” and a few words concern ingits practical aspect follow later.
The computer is indispensable for literature searches. The U.S. National Library of Medicine publishes PubMed for this purpose, which the more elderly researchers still know as MedLine. It contains a list of all articles over the past decades that have been found in the important and relatively important medical and scientific journals. Listings usually also contain abstracts of the articles, andentries are regularly updated.
There is specific software for the analysis of DNA sequences, which is especially near to the heart of molecular biologists. It can also be considered a tool for the self-gratification of molecular biologists, with which they can kill time between individual cloning procedures. Some programs can examine a polymerase chain reaction (PCR) primer for its usefulness. Some programs can be used for sequence analysis and predictions and used to search for functional areas in the DNA or the proteins coded by them. With other programs, the experimenter can look for sequences that demonstrate homologies to his or her own.
The Internet is particularly useful for searching for sequences. The multitude of sequences that are published every day quickly led to the idea of sequence data banks in which the researcher can rummage. The most important are the GenBank of the National Center for Biotechnology Information (NCBI) (http://www.ncb.nlm.nih.gov) and the EMBL bank of the European Molecular Biology Organisation (http://www.ebi.ac.uk), which compare one another’s data daily and can therefore be considered as equivalent. Because the search for homologous sequences by hand is no longer possible, these institutions offer search programs for the databases, primarily the BLAST programs (Basic Local Alignment Search Tool), to which experimenters have access by way of email or over the Internet. Many additional databases with different emphases may occasionally be of interest to the molecular biologist, such as that for the Online Mendelian Inheritance in Man(OMIM), which deals with genetic illnesses (http://www.ncbi.nlm.nih.gov/Omim); SWISSPROT,the classic protein database (http://www.expasy.ch/sprot); or GeneCards, a data bank of humangenes with information concerning the function of the coded proteins and their role in diseases(http://bioinformatics/weizmann.ac.il/cards).
The databases occasionally spare the experimenter the cloning process. A specific sequence can easily be searched for in the sequence banks, and if it is found, the clone can be ordered. In these madtimes, there are institutions that isolate clones indiscriminately from cDNA banks, add sequences,and then deposit these sequences in data banks. These sequences are marked as expressed sequence tags (EST), and various EST banks and the respective clones are accessible for researchers (e.g., thedbEST data bank at http://www.ncbi.nlm.nih.gov/dbEST/index.html). In this way, a researcher can get hold of genes that have been previously unknown without having to do any cloning. From the several million human EST sequences available, an attempt has already been made to obtain an overview of the underlying genes (http://www.ncbi.nlm.nih.gov/UniGene/index.html). Some bacteria, such as Saccharomyces cerevisiae and Caenorhabditis elegans and larger organisms, such as Drosophilamelanogaster, Homo sapiens, or Mus musculus, have practically been fully sequenced so that the end of any new discoveries is gradually reaching a tangible proximity.
Regardless of what Microsoft says, word processing programs such as Word are conceived for writing letters and smaller papers, not for diplomas or for doctoral theses. Although these programs offer all kinds of comfort, such as automatic numbering and colorful graphics, longer texts that takefull advantage of all of the possibilities of the program usually have increasing problems, and you may experience a total collapse, most likely when the work is practically perfect. You can chop upthe text into smaller segments of approximately 50 pages as a precaution, or you can purchase a professional layout program.
For many, the second most important use of the computer is email (electronic mail ). With email, you can keep a collaboration alive, arrange to meet people, discuss live with specialists sitting even in some other country and so on.
There is also the Internet. Presumably, every child is aware of this concept. It is the world of colorful pictures and web sites that can be surfed. The Internet earns the commendation “of utmost value to the researcher,” and a few words concern ingits practical aspect follow later.
The computer is indispensable for literature searches. The U.S. National Library of Medicine publishes PubMed for this purpose, which the more elderly researchers still know as MedLine. It contains a list of all articles over the past decades that have been found in the important and relatively important medical and scientific journals. Listings usually also contain abstracts of the articles, andentries are regularly updated.
There is specific software for the analysis of DNA sequences, which is especially near to the heart of molecular biologists. It can also be considered a tool for the self-gratification of molecular biologists, with which they can kill time between individual cloning procedures. Some programs can examine a polymerase chain reaction (PCR) primer for its usefulness. Some programs can be used for sequence analysis and predictions and used to search for functional areas in the DNA or the proteins coded by them. With other programs, the experimenter can look for sequences that demonstrate homologies to his or her own.
The Internet is particularly useful for searching for sequences. The multitude of sequences that are published every day quickly led to the idea of sequence data banks in which the researcher can rummage. The most important are the GenBank of the National Center for Biotechnology Information (NCBI) (http://www.ncb.nlm.nih.gov) and the EMBL bank of the European Molecular Biology Organisation (http://www.ebi.ac.uk), which compare one another’s data daily and can therefore be considered as equivalent. Because the search for homologous sequences by hand is no longer possible, these institutions offer search programs for the databases, primarily the BLAST programs (Basic Local Alignment Search Tool), to which experimenters have access by way of email or over the Internet. Many additional databases with different emphases may occasionally be of interest to the molecular biologist, such as that for the Online Mendelian Inheritance in Man(OMIM), which deals with genetic illnesses (http://www.ncbi.nlm.nih.gov/Omim); SWISSPROT,the classic protein database (http://www.expasy.ch/sprot); or GeneCards, a data bank of humangenes with information concerning the function of the coded proteins and their role in diseases(http://bioinformatics/weizmann.ac.il/cards).
The databases occasionally spare the experimenter the cloning process. A specific sequence can easily be searched for in the sequence banks, and if it is found, the clone can be ordered. In these madtimes, there are institutions that isolate clones indiscriminately from cDNA banks, add sequences,and then deposit these sequences in data banks. These sequences are marked as expressed sequence tags (EST), and various EST banks and the respective clones are accessible for researchers (e.g., thedbEST data bank at http://www.ncbi.nlm.nih.gov/dbEST/index.html). In this way, a researcher can get hold of genes that have been previously unknown without having to do any cloning. From the several million human EST sequences available, an attempt has already been made to obtain an overview of the underlying genes (http://www.ncbi.nlm.nih.gov/UniGene/index.html). Some bacteria, such as Saccharomyces cerevisiae and Caenorhabditis elegans and larger organisms, such as Drosophilamelanogaster, Homo sapiens, or Mus musculus, have practically been fully sequenced so that the end of any new discoveries is gradually reaching a tangible proximity.
Computer Care
Sometimes the computer systems may fail to function due to carelessness. So technical experts can be found to provide instruction about the computer. Individual should be known who is responsible for installing new versions of a program. If you have some influence on the decision, strive to see that the old version survives. If possible, let the others try it out to see whether the new version offers any advantages or has problems involved in its use. A common problem, for instance, is that the new version consumes far more hard drive space and memory than the old version, which can overload the computer. Why should you struggle with such difficulties if the old program did everything you wanted?
A common error of non computer specialists is their trust in the computer and its components. Everyone thinks that computers are very reliable. That is the case so long as no one needs them. When you are in the final phase of your doctoral thesis—100 pages have been written, a mere 30 pages are still lacking, and the figures and layout are all correct—disaster is guaranteed to occur. This is the time when the hard disk crashes.
Always store back-up copies of the most important files. Memory sticks can be used for this purpose, although it is safer to store back-up copies on another hard disk or burn a CD. Another popular sin is working directly on memory sticks. They are robust (more robust thanfloppy disks used to be), handy, and allow you to work on different computers without leaving you with a flood of copies of different stages of your work. Although being pretty reliable, they have still a higher tendency to fail than hard disks, they are slower (which can induce you to save your magnum opus less often than recommendable), and they can easily be unplugged, sometimes with unforeseeable consequences. To prevent problems, a back-up copy should always be saved on a well-preserved hard disk.
At some point, even the longest work is completed and must then be archived. A CD-ROM is the most suitable storage material. If you would like to take a look at your masterpiece in another 5 or 10years, it is advisable to keep an old-fashioned, printed paper version somewhere. You can write what you like on paper.
Special characters, including ä ö ü ß, often cannot be used, particularly when writing to English speaking foreign countries, and the recipient must struggle through hieroglyphics such as /f{. or*{/ in the middle or at the end of some words.
If all prognoses about the Internet were correct, we would no longer have to leave our homes,because we could do all tasks through a simple click of the mouse. Somehow, everything worked out differently.The Internet is a vast number of computers that communicate with one another over a networkof lines, using a directory to assess who else is connected and how to reach them. If researcher A ina country wants to look at an Internet web site that has been prepared by researcher B in some other country, he or she uses the Internet address to view the data. The first computer sends a corresponding messageto computer Tom, which then transmits this to computer Dick and so forth, until it ultimately arrives at computer Harry. This computer can then send data back using the same principle, although not definitely according to the same route. The Internet is a network that functions according to the principle that “all roads lead to Rome,” and it is surprisingly fast. As in real life, however, traffic jams occur on the data highway. Most are small and lead to delays of only seconds, although sometimes, nothing functions as it should.
The Internet offers inestimable advantages if you learn how to use it correctly. The largest problem is too much information. The network offers practical search services such as Google. Searches often produce dozens to tens of thousands of Internet addresses for each keyword typed in, and results may or may not be close to what you were searching for. Most of this information, however, is uninteresting and time consuming. It is best off to spend the free moments of the day relaxed in front of the computer and to go on a voyage of discovery. If you encounter something useful, the address can be stored with a bookmark. In the course of time, you can acquire a collection of useful addresses. With this healthy outlook, the Internet becomes a useful resource with which you can obtain information within seconds. However,if you do not heed this advice, surfing the network will turn out to be a great waste of time.
For researchers, the Internet is interesting because of the databases already mentioned; the newsgroups, which offer suggestions from like-minded individuals for solving problems (it is sometimes very motivational to see that many around the globe suffer from the same problems as you do);home pages from institutes, where you can learn what the people do there; sites where shareware or freeware programs can be obtained; online versions of scientific magazines; and much more.Over time, using computers can provide more knowledge and help to develop a certain level of expertise.
A common error of non computer specialists is their trust in the computer and its components. Everyone thinks that computers are very reliable. That is the case so long as no one needs them. When you are in the final phase of your doctoral thesis—100 pages have been written, a mere 30 pages are still lacking, and the figures and layout are all correct—disaster is guaranteed to occur. This is the time when the hard disk crashes.
Always store back-up copies of the most important files. Memory sticks can be used for this purpose, although it is safer to store back-up copies on another hard disk or burn a CD. Another popular sin is working directly on memory sticks. They are robust (more robust thanfloppy disks used to be), handy, and allow you to work on different computers without leaving you with a flood of copies of different stages of your work. Although being pretty reliable, they have still a higher tendency to fail than hard disks, they are slower (which can induce you to save your magnum opus less often than recommendable), and they can easily be unplugged, sometimes with unforeseeable consequences. To prevent problems, a back-up copy should always be saved on a well-preserved hard disk.
At some point, even the longest work is completed and must then be archived. A CD-ROM is the most suitable storage material. If you would like to take a look at your masterpiece in another 5 or 10years, it is advisable to keep an old-fashioned, printed paper version somewhere. You can write what you like on paper.
Special characters, including ä ö ü ß, often cannot be used, particularly when writing to English speaking foreign countries, and the recipient must struggle through hieroglyphics such as /f{. or*{/ in the middle or at the end of some words.
If all prognoses about the Internet were correct, we would no longer have to leave our homes,because we could do all tasks through a simple click of the mouse. Somehow, everything worked out differently.The Internet is a vast number of computers that communicate with one another over a networkof lines, using a directory to assess who else is connected and how to reach them. If researcher A ina country wants to look at an Internet web site that has been prepared by researcher B in some other country, he or she uses the Internet address to view the data. The first computer sends a corresponding messageto computer Tom, which then transmits this to computer Dick and so forth, until it ultimately arrives at computer Harry. This computer can then send data back using the same principle, although not definitely according to the same route. The Internet is a network that functions according to the principle that “all roads lead to Rome,” and it is surprisingly fast. As in real life, however, traffic jams occur on the data highway. Most are small and lead to delays of only seconds, although sometimes, nothing functions as it should.
The Internet offers inestimable advantages if you learn how to use it correctly. The largest problem is too much information. The network offers practical search services such as Google. Searches often produce dozens to tens of thousands of Internet addresses for each keyword typed in, and results may or may not be close to what you were searching for. Most of this information, however, is uninteresting and time consuming. It is best off to spend the free moments of the day relaxed in front of the computer and to go on a voyage of discovery. If you encounter something useful, the address can be stored with a bookmark. In the course of time, you can acquire a collection of useful addresses. With this healthy outlook, the Internet becomes a useful resource with which you can obtain information within seconds. However,if you do not heed this advice, surfing the network will turn out to be a great waste of time.
For researchers, the Internet is interesting because of the databases already mentioned; the newsgroups, which offer suggestions from like-minded individuals for solving problems (it is sometimes very motivational to see that many around the globe suffer from the same problems as you do);home pages from institutes, where you can learn what the people do there; sites where shareware or freeware programs can be obtained; online versions of scientific magazines; and much more.Over time, using computers can provide more knowledge and help to develop a certain level of expertise.
Ref : Molecular Biology and Genomics (Elsevier, 2007)
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