• Matlab

  • Referenced in 8309 articles [sw00558]
  • test and measurement, computational finance, and computational biology. More than a million engineers and scientists...
  • CGAL

  • Referenced in 274 articles [sw00118]
  • design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, mesh...
  • LISREL

  • Referenced in 271 articles [sw06514]
  • social sciences, management sciences, behavioral sciences, biological sciences, educational sciences and other fields to empirically...
  • KEGG

  • Referenced in 141 articles [sw13866]
  • high-level functions and utilities of the biological system, such as the cell, the organism ... computer representation of the biological system, consisting of molecular building blocks of genes and proteins ... information (health information) as perturbations to the biological system...
  • FGb

  • Referenced in 223 articles [sw00286]
  • used in various applications (Robotic, Signal Theory, Biology, Computational Geometry, . . . ) and more recently...
  • Bio-PEPA

  • Referenced in 93 articles [sw01361]
  • order to handle some features of biological models, suchas stoichiometry and the use of general ... intermediate, formal, compositional representation of biological systems, on which different kindsof analysis can be carried ... Finally, we show the translation of a biological model into thenew language and we report...
  • BLAST

  • Referenced in 114 articles [sw17334]
  • Tool. BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein...
  • PSI-BLAST

  • Referenced in 102 articles [sw17324]
  • much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used...
  • DSTool

  • Referenced in 98 articles [sw06719]
  • systems arise in many disciplins of physics, biology and chemistry - basically always whenever something...
  • Gromacs

  • Referenced in 86 articles [sw04128]
  • also using it for research on non-biological systems, e.g. polymers...
  • CMA-ES

  • Referenced in 81 articles [sw05063]
  • broadly based on the principle of biological evolution, namely the repeated interplay of variation...
  • SHOGUN

  • Referenced in 65 articles [sw03517]
  • this toolbox in several applications from computational biology, some of them coming with no less...
  • PMA

  • Referenced in 65 articles [sw19126]
  • data. Statistical Applications in Genetics and Molecular Biology 8(1): Article...
  • VMD

  • Referenced in 62 articles [sw18651]
  • designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid...
  • PHYLIP

  • Referenced in 60 articles [sw07694]
  • Genome Sciences and the Department of Biology at the University of Washington, contain information...
  • DAVID

  • Referenced in 30 articles [sw17292]
  • DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large ... condense a list of genes or associated biological terms into organized classes of related genes ... biology, called biological modules. This organization is accomplished by mining the complex biological co-occurrences ... terms into a manageable number of biological modules for efficient interpretation of gene lists...
  • BIOCHAM

  • Referenced in 38 articles [sw09927]
  • Biocham) is a modelling environment for systems biology, with some unique features for static analysis ... formalize the temporal properties of a biological system and validate models with respect to such...
  • PAUP*

  • Referenced in 30 articles [sw07834]
  • well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse ... conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis ... even more indispensable tool in comparative biological analysis than were previous editions of the program...
  • Pse-in-One

  • Referenced in 23 articles [sw22407]
  • protein sequences. With the avalanche of biological sequences generated in the post-genomic ... most challenging problems in computational biology is how to effectively formulate the sequence ... biological sample (such as DNA, RNA or protein) with a discrete model or a vector ... often difficult for users to formulate the biological sequences according to their desired features...
  • Cell-PLoc

  • Referenced in 27 articles [sw09126]
  • proteins is important to molecular cell biology, proteomics, system biology and drug discovery. To provide ... interesting, because they may have some special biological functions intriguing to investigators in both basic...