Bioinformatics standardization

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

There are many products based on these life sciences standards, such as the aforementioned gene expression standard that is used in Rosetta Merck s Resolver product and the European Bioinformatics Institute s (EBI) Array-Express database. The LECIS (Laboratory Equipment Control Interface Specification) standard is used by Creon as part of their Q-DIS data standard support (note that one of the authors was the finalization task force chairperson for this standard). 

Stanislaus, R., Jiang, L.H., Swartz, M., Arthur, J. Almeida, J.S. (2004). An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. BMC Bioinformatics 5, 9. 

The use of PIR compounds to study protein interactions is a significant advance over the use of standard homobifunctional crosslinkers. The unique design of the PIR reagent facilitates deconvolution of putative protein interaction complexes through a simplified mass spec analysis. The software can ignore all irrelevant peak data and just focus analysis on the two labeled peptide peaks, which accompany the reporter signal of appropriate mass. This greatly simplifies the bioinformatics of data analysis and provides definitive conformation of protein-protein crosslinks. 

To make full use of microarray data it is necessary that data of published microarray experiments be made available to other researchers for comparison purposes. To this end, the Minimum Information About a Microarray Experiment (MIAME) (31) guidelines have been developed at the European Bioinformatics Institute (EBI). This standard describes the minimum information required to ensure that microarray data can be easily interpreted, and that results derived from its analysis can be independently verified. 

Once you have a standard Linux installation, you need to download and install some basic bioinformatics software. For the examples here, all you need are listed below... 

XML technologies [22, 23] have become a general standard for storing and converting all kinds of data and technically more robust solutions than mmCif based on XML, such as PROXIML [24], were proposed but still not accepted by the Research Collaboratory for Structural Bioinformatics. 

Table 7 Relative Size of Standard Bioinformatics Resources...

The MIAME standard defines the minimum information investigators must report for a microarray experiment to be reproduced. The MAGE standard was born partially from MIAME, and the European Bioinformatics Institute used MIAME and MAGE to guide the development of ArrayEx-press, their public genomic data repository (34). Sample annotation lies at the heart of MIAME, underscoring the need to understand as completely as possible the experimental conditions that may influence the microarray data. Many journals that publish microarray data require the submission of MIAME-supportive microarray data to a public genomic data repository as a condition of publication. These typically include submission of protocols species, strains, and sex used for in vivo studies cell line name and culture conditions for in vitro studies, and other relevant information. 

At present, there are advanced difference gel electrophoresis (DOGE) Systems and 2-D fluorescence difference gel electrophoresis (2-D DIGE) which enable the analyst to use simultaneously modern (more precise) methods of fluorescent analysis with 2-D electrophoresis (using internal patterns), aided by a fully integrated bioinformatics system. Such systems allow more complete differential protein analysis, while the application of internal standards eliminates differentiation between the intervals, thus ensuring that even the smallest differences will be detected irrespective of the multitude of components. This guarantees reproducibility of results and their statistical reliability. Such assays are one of the platforms employed in the research based on the proteomics method. 

Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23 2760-2767... 

The results and considerations of the pilot phase will be used as the basis for the activities in the main phase. The network and the bioinformatics infrastructure will allow the performance of standardized differential analysis of neurodegene-rative diseases. 

The need for standardization, most notably in bioinformatics, e.g., data formats and exchange, is stressed in the chapter Proteomic Data Standardization,... 

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