Analysis tools

ANALYSIS TOOLS

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Table of contents :

In silico analysis techniques (bioinformatics) : see also informatics

Literature researches
Nucleic acids tools
Proteids tools
Other databases, database collections and tools
Statistics and epidemiology

In vitro analysis techniques

In vivo analysis techniques
Ex vivo analysis techniques (i.e. : in vitro => in vivo)
Quality control

In order to understand life phenomena you have to combine :

analytical chemistry
genomic engineering
bioinformatics : the organization and use of biological information, particularly computer-driven processing and analysis of data and databases in the fields of molecular biology and genetics

One of the ultimate goal of life science is to gain a comprehensive understanding of the cell, the smallest unit of life. Realistically speaking, however, it is probably impossible for human intelligence to map out how the metabolites inside of the cell act, because understanding the cell means knowing how each part functions in coordination with the system as a whole, and under what conditions, and how much change occurs. Just thinking about how the thousands of metabolites in different locations inside of the cell interact, under these conditions, is enough to make you dizzy. Whether or not computer simulation is the most appropriate way of doing this, I think that at present time there are no other options. It is also important to conduct experiments for the sake of quantification and simulation of the dynamic changes in cells. In short, various information is required for making models of cells by computer, and this information can only be corroborated experimentally. Biology is set to become highly quantitative in the 21st century. It will become a computer-intensive discipline. Software infrastructure is another critical component of system biology research. Although attempts have been made to build simulation software and to make use of the many analysis and computing packages originally designed for general engineering purposes, there is no common infrastructure or standard to enable integration of these resources :

XML-based computer-readable model definition that enables models to be exchanged between software tools.

CellML, developed by the Bioengineering Institute at the University of Auckland, incorporates existing languages including MathML and RDF to encode mathematical information
Bioinformatic Sequence Markup Language (BSML) v.3.1
Systems Biology Mark-up Language (SBML) : a "species" is a term defined by SBML as "an entity that takes part in reactions", and it distinguishes the different states that are caused by enzymatic modification, combination, dissociation, and translocation. To distinguish the different states of a component in the same compartment in detail, we only need to assign a unique name to each state using suitable subscripts. For example, states of the protein that translocates from cytosol to plasma membrane can be distinguishable by names such as "XX_cyt" and "XX_pm". Since SBML is a machine-readable format, all the information can be used for a range of computational analysis, including computer simulation.

ERATO Systems Biology Workbench (SBW) is built on SBML and provides a framework of modular open-source software for systems biology research. With the ongoing rapid increase in both volume and diversity of 'omic' data (genomics, transcriptomics, proteomics, and others), the development and adoption of data standards is of paramount importance to realize the promise of systems biology. A recent trend in data standard development has been to use extensible markup language (XML) as the preferred mechanism to define data representations. But the syntactic and document-centric XML cannot achieve the level of interoperability required by the highly dynamic and integrated bioinformatics applications. Semantic web technologies (RDF), as recommended by the World Wide Web consortium (W3C), expand current data standard technology for biological data representation and management^ref.

Biological Abstraction Layer for Simulation Analysis (BALSA) is a project of the Cell Systems Initiative of the University of Washington. BALSA is a symbolic language for representing biological processes, including cell signaling. One of the examples includes the canonical Wnt/beta-catenin Pathway from STKE. BALSA is currently a prototype of a Java-based cell systems modeling environment prototype. A cursory explanation of BALSA and its support software, Bioglyphics
CellDesigner : modeling tool for biochemical networks. Designed to be compliant with SBML format
Cytoscape : an open-source bioinformatics software platform for visualizing molecular interaction networks. Can integrate the network interactions with gene-expression profiles
PathwayStudio : a desktop or client-server software package for visualization and analysis of biological pathways. Works with the company's ResNet database of over 1,000,000 functional relationships
SRS (Sequence Retrieval System) Bioinformatics Software : utilizes SRS Web Services technology to pull data from different sources. Pathway editor can visualize relationships among data.

How quickly data can be written to your hard drive ? about 435,000 million bits a second. Electron pulses lasting 2.3 picoseconds or less are too short to reliably record a bit of computer information. But such a rate is still a thousand times faster than we can achieve in state-of-the-art magnetic devices today.
information theory : a system for analyzing, chiefly by statistical methods, the characteristics of communicated messages and the systems that encode, transmit, distort, receive, and decode them.

Web resources

dmoz Open Directory Project : Methods and Techniques in Biology
dmoz Open Directory Project (ODP) : Biotechnology
The Virtual Library - Biotechnology
bioWWW
Society for In Vitro Biology (SIVB)
Comprehensive protocol collection at Dartmouth University
Protocols at Weizmann Institute, Israel
Molecular Biology Protocols at NWFSC, USA
Arkitek : Visual Specialists for Science and Technology
bioinformatics

Encyclopedia of Life project (EOL) at San Diego Supercomputer Center, University of California, seeks to catalog the complete proteome of every living species in a flexible, powerful reference system. It is an ideal application for the TeraGrid initiative. In the meantime, users can catch a glimpse of EOL's power as applied to Arabidopsis
National Center for Biotechnolology Information (NCBI), NLM, NIH

Entrez
The NCBI Handbook [free at NCBI BookShelf !]
The NCBI C++ Toolkit; 2003 April [free at NCBI BookShelf !]

medical calculators :

The Medical Algorithms (MedAl) Project : > 6100 computation, formula, survey, or look-up table, useful in healthcare, organized into 45 chapters
Medical Calculator at Cornell University, USA