Introduction to Bioperl
Bioperl has recently reached version 1.0, first said that BiOperl.org, the organization was formally established in 1995, which has been in the informal group for many years before this, and now he has formed an international developer association, these Developers have developed Perl tools for open source for bioinformatics, genomics, and life science research.
The organization's supporters and pushers are Open BioInformatics Foundation. Their partners also have Biojava.org, Biopython.org, DAS, Bioruby.org, Biocorba.org, Ensembl, and Emboss.
Bioperl's servers provide the following services for the software based on Perl-based modules, scripts, web couplers.
Bioperl has now developed into a remarkable international free software development plan, which accelerates the development of biological information, genomics, and other life scientific research in bioinformatics. Recently, the Bioperl 1.0 version was officially released, which lasted for seven years, and the results were very good. Bioperl 1.0 includes 832 files, 93 Script, rich feature, all open. It is a weapon for bioinformatics research. Detailed content You can visit www.bioperl.org.
Bioperl's expansion of the PERL is specifically used for biological information, and naturally also inherits the numerous advantages of Perl.
First. PERL powerful regular representation (REGLAR EXPRESSION) alignment and string operation makes this work simple and no other language. Perl is very good at cutting, twisting, twisted, flat, summarizing, and other operational text files. Most of the biological materials is a text file: species name, species, genetic or sequence annotation, assessment, directory consultation, and even DNA sequences are also class. It is now exchanging to exchange in the form of a text file, but the incompatible data format biological information is a very headache. The advantages of this aspect of Perl can solve many problems in this regard.
Second. Perl can be faulty. Biological data is usually incomplete, error or error may be generated from the production of data. In addition, a certain value field of biological data can be ignored, may be empty, or a certain field is some The value is expected to appear several times (for example, an experiment may be repeated), or the data is manually input, so there is an error. Perl does not mind that a value is empty or a strange character. The formal representation can be written to take out and correct the error. Of course, this flexibility may also be bad.
Also, Perl is the component orientation. Perl encourages people to write their software into a small module, whether using Perl library modules or orthodoxical ways. External programs can be easily integrated into the Perl program, leaning against a pipe (PIPE), system call, or socket. The dynamic loader introduced by Perl5 allows people to use C's functions or allow the entire programmed library to be used in the Perl direct translator. Recent results is that smart crystals around the world will be included in a group of modules, called "Bioperl" (see Perl Journal) Perl easy to write and can be developed quickly. The direct translator allows you to declare all your function patterns and data type. When an undefined group is called, it will only cause an error, and the decentralizer can cooperate well with Emacs and let you use it. Comfortable conversation model. Perl is a good prototype language. Because it is fast and dirty, the original model with Perl constructs a new calculation is written directly into a fast-friendly language. Sometimes the result is that Perl is already fast enough, so the program does not need to be transplanted; more case is that someone can write a small core program with C, programming into dynamic loaded modules or external executable, The other part then is done with Perl. Examples of this section can be found in http://waldo.wi.mit.edu/ftp/distribut/software/rhmapper/). One thing to emphasize is that Perl is very good in writing web CGIs, and the importance increases after the experiments published information on the network. I used Perl's experience in the Central Environment. It is worthy of praise from beginning to end. However, I found that Perl also has its problems. Its loose program style causes many errors that are caught in other stringent languages. For example, Perl allows you to use a variable before being specified, this is a very useful feature when you need it, but it is a disaster when you are a simple misconscious identification name. Similarly, it is easy to forget to declare the region variables in a single function, causing accidentally changed to the whole country variable. Finally, the deficiencies of Perl are to establish a graphical user interface. Although UNIX faithful believans can be done in command mode, most end users do not agree. Windows, menu, bounce pattern have become necessary.
Until recently, until recently, Perl's user interface (GUI) is still immature. However, the efforts of Nick Ing-Simmons make the integration of Perltk (PTK) make it possible to be able to use Perl-driven user interfaces in X-WINDOW. My partner and I have written a few PTK based applications in the Mit Gene Center for internet users, and are a satisfactory experience from head to tail. Other genetics are larger using PTK, in some places have become the main productivity.
