Applications of Computational Tools

Information science and computational science provide essential tools for next generation biological science efforts, from managing large amounts of data, focusing the direction of experimental studies to providing knowledge and insight that cannot otherwise be obtained in biological phenomena.

Tool Challenges for Computer Science

Data Representation

  • Next-generation genome annotation system with accuracy equal to or exceeding the best human predictions
  • Mechanism for multimodal representation of data

Analysis Tools

  • Scalable methods of comparing many genomes
  • Tools and analyses to determine how molecular complexes work within the cell
  • Techniques for inferring and analyzing regulatory and signaling networks
  • Tools to extract patterns in mass spectrometry datasets
  • Tools for semantic interoperability


  • Tools to display networks and clusters at many levels of detail
  • Approaches for interpreting data streams and comparing high-throughput data with simulation output


  • Good software-engineering practices and standard definitions
  • Standard ontology and data-exchange format for encoding complex types of annotation


  • Large repository for microbial and ecological literature relevant to the "Genomes to Life" effort
  • Big relational database derived by automatic generation of semantic metadata from the biological literature
  • Databases that support automated versioning and identification of data provenance
  • Long-term support of public sequence databases

Three Generic Types of Computational Tools

  • Databases and data management tools to integrate large amounts of heterogeneous biological data
  • Presentation tools that help users comprehend large datasets
  • Algorithms to extract meaning and useful information from large amounts of data

Open source software provides a platform for computational biology where everyone can access and benefit from software developed in research.

Bioinformatics Software and Tools
GALAXY Clustal FastTree
Ascalaph Designer FastQC Harvest
AutoDock SPAdes MEGA
BioJava Velvet PathogenFinder
Integrated Genome Browser Burrows Wheeler Aligner DNASTAR Lasergene
Bioconductor Pilon SeqBuilder Pro
GenePattern BLAST Sequencher
Geworkbench QUAST Geneious
GROMACS Genome Analysis Toolkit CLC Workbench

Applications of Software in Computational Biology


  1. National Research Council (US) Committee on Frontiers at the Interface of Computing and Biology; Wooley JC, Lin HS, editors. Catalyzing Inquiry at the Interface of Computing and Biology. Washington (DC): National Academies Press (US); 2005. 4, Computational Tools.
* For Research Use Only.