By Kevin Strange (auth.), Kevin Strange (eds.)
Molecular biology has pushed a strong reductionist, or “molecule-c- tric,” method of organic learn within the final half the twentieth century. pink- tionism is the try and clarify advanced phenomena through defining the useful houses of the person elements of the procedure. Bloom (1) has spoke of the post-genome sequencing period because the finish of “naïve reductionism. ” crimson- tionist tools will remain a vital portion of all organic examine efforts, yet “naïve reductionism,” the idea that reductionism on my own can result in a whole knowing of residing organisms, isn't tenable. Organisms are basically even more than the sum in their elements, and the habit of complicated physiological procedures can't be understood just by realizing how the components paintings in isolation. platforms biology has emerged within the wake of genome sequencing because the s- cessor to reductionism (2–5). The “systems” of platforms biology are outlined over a large span of complexity starting from macromolecules that have interaction to hold out a particular job to complete organisms. structures biology is integrative and seeks to appreciate and are expecting the habit or “emergent” homes of complicated, multicomponent organic techniques. A systems-level characteri- tion of a organic technique addresses the subsequent 3 major questions: (1) What are the elements of the method (i. e.
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Extra info for C. elegans: Methods and Applications
Sample text
8 9 my @genes = $DB->fetch(-query=> 10 qq{find Gene where Species=”Caenorhabditis elegans”}); 11 12 foreach my $gene (@genes) { 13 my $name = $gene->Public_name || $gene; 14 my @alleles = $gene->Allele; 15 print join(“\t”,$name,@alleles),”\n”; 16 } This script uses standard Perl notation (see Note 3), executing the following steps. Line 3 makes functions provided by the AcePerl library available to the script. Lines 5–7 establish a connection to the appropriate database, exiting the script if a connection cannot be established.
4. org [4]) provides several options for viewing syntenic blocks between C. elegans and C. briggsae graphically. First, in the Genome Browser, syntenic blocks are displayed under the “briggsae alignments” track. Within the syntenic blocks, WABA-classified “coding” regions appear in dark blue, “strong” regions in light blue, and “weak” regions in gray. Because syntenic blocks can contain gaps for which there is no WABA nucleotide-level alignment, they may not be fully continuous. A dashed gray line represents these gaps in a syntenic block.
Elegans: Methods and Applications Edited by: K. , Totowa, NJ 31 32 Harris and Stein and presenting data are split between the groups. Caltech is primarily responsible for systematic curation of data from the published literature; WashU and Sanger are each responsible for curating half of the genome sequence (and associated gene models); CSHL is in charge of user-interface development and management of the website. Additionally, Sanger is responsible for assembling the release version of the database.