Biointelligence

November 10, 2009

BASE – A software for Microarray Data Management and Analysis

Filed under: Bioinformatics,Microarray — Biointelligence: Education,Training & Consultancy Services @ 4:27 am
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Microarray techniques produce large amounts of data in many different formats and experiment sizes are growing with more samples analysed in each experiment. Samples are collected over long time and microarray analysis is performed asynchronously and re-analysed as more samples are hybridised. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. Particularly for microarray service facilities, where researchers deposit samples for experimentation, information tracking becomes vital for a subsequent data delivery back to the researchers. To meet the information tracking and data analysis challenges involved in microarray experiments BASE has been implemented.

BASE (Bioarray Software Environment) is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. It is a MIAME (Minimum Information About a Microarray Experiment guidelines) compliant application designed for microarray laboratories looking for a single point of storage for all information related to their microarray experimentation. BASE is a multi-user local data repository that features a web browser user interface, laboratory information management system (LIMS) for biomaterials and array production, annotations, hierarchical overview of analysis, and integrates tools like MultiExperiment Viewer (MEV) and GenePattern.

BASE is an annotable microarray data repository and analysis application providing researchers with efficient information management and analysis. BASE stores all microarray experiment related data, biomaterial information, and annotations regardless if analysis tools for specific techniques or data formats are readily available. As new techniques becomes available software applications should be expendable and modifiable to support changed needs. Moreover, it is an open source software and is freely available.

BASE website: http://base.thep.lu.se

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October 28, 2009

Useful Bioinformatics Links

Here are some useful and handy bioinformatics links which would aid in study of bioinformatics and various related fields:

http://www.cellbiol.com/

http://www.expasy.org/links.html

http://www.biochemweb.org/databases.shtml

http://bioinformatics.byu.edu/

http://www-personal.umich.edu/~lpt/chemlinks.htm

http://www.sciencegateway.org/tools/index.html

http://molbiol-tools.ca/

http://dorakmt.tripod.com/mtd/biomed.html

http://www.bio.ku.dk/mundy/links.htm

http://users.breathe.com/hachen/mol_biol_sites.html

http://www.whitney.ufl.edu/resources/molecular-links.htm

http://bioinformatics.ws/index.php/Bioinformatics_tools_and_algorithms

http://fruitfly4.aecom.yu.edu/molbio.html

http://www.biologie.uni-erlangen.de/mpp/pages/tools_prot.html

http://staff.umt.edu.my/~cha_ts/Cha%20Bioinfo.html

September 22, 2009

Minimum Information about a Microarray Experiment

Filed under: Bioinformatics,Microarray — Biointelligence: Education,Training & Consultancy Services @ 11:20 am
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After genome sequencing, DNA microarray analysis has become the most widely used source of genome scale data in the life sciences. Microarray expression studies are producing massive qunatities of gene expression and other functional genomics data, which priomise to provide an insight into gene function and inetractions within and across metabolic pathways. Unlike genome sequence data, however, which have standard formats for presentation and widely used tools and databases, much of the microarray daa generated so far remain inaccessible.

To make this information accesible in a proper format MIAME (Minimum Information About a Microarray Experiment) was introduced. MIAME format was introduced to address the ned for comprehensive annotation necessary to interpret the results of microarray data. It is platform independent but includes essential evidence about how the gene expression level measurements have been obtained.

Although the goal of MIAME is to specify only the content of the information and not the technical format, MIAME includes recommendations for which parts of the information should be provided as controlled vocabularies. MIAME includes a description of the six sections which need to be included:

1. Experimental Design
2. Array Design
3. Samples
4. Hybridizations
5. Measurements
6. Normalization controls

This specific format would really make it easy to interpret microarray data obtained from various experiments.
To read more on MIAME click here-  http://www.mged.org/Workgroups/MIAME/miame.html

 

 
After genome sequencing, DNA microarray analysis has become the most widely used source of genome scale data in the life sciences. Microarray expression studies are producing massive qunatities of gene expression and other functional genomics data, which priomise to provide an insight into gene function and inetractions within and across metabolic pathways. Unlike genome sequence data, however, which have standard formats for presentation and widely used tools and databases, much of the microarray daa generated so far remain inaccessible.

To make this information accesible in a proper format MIAME (Minimum Information About a Microarray Experiment) was introduced. MIAME format was introduced to address the ned for comprehensive annotation necessary to interpret the results of microarray data. It is platform independent but includes essential evidence about how the gene expression level measurements have been obtained.

Although the goal of MIAME is to specify only the content of the information and not the technical format, MIAME includes recommendations for which parts of the information should be provided as controlled vocabularies. MIAME includes a description of the six sections which need to be included:

1. Experimental Design
2. Array Design
3. Samples
4. Hybridizations
5. Measurements
6. Normalization controls

This specific format would really make it easy to interpret microarray data obtained from various experiments.
To read more on MIAME click here-  http://www.mged.org/Workgroups/MIAME/miame.html

 

 
After genome sequencing, DNA microarray analysis has become the most widely used source of genome scale data in the life sciences. Microarray expression studies are producing massive qunatities of gene expression and other functional genomics data, which priomise to provide an insight into gene function and inetractions within and across metabolic pathways. Unlike genome sequence data, however, which have standard formats for presentation and widely used tools and databases, much of the microarray daa generated so far remain inaccessible.

To make this information accesible in a proper format MIAME (Minimum Information About a Microarray Experiment) was introduced. MIAME format was introduced to address the ned for comprehensive annotation necessary to interpret the results of microarray data. It is platform independent but includes essential evidence about how the gene expression level measurements have been obtained.

Although the goal of MIAME is to specify only the content of the information and not the technical format, MIAME includes recommendations for which parts of the information should be provided as controlled vocabularies. MIAME includes a description of the six sections which need to be included:

1. Experimental Design
2. Array Design
3. Samples
4. Hybridizations
5. Measurements
6. Normalization controls

This specific format would really make it easy to interpret microarray data obtained from various experiments.
To read more on MIAME click here-  http://www.mged.org/Workgroups/MIAME/miame.html

September 11, 2009

List of Companies working on Microarrays and related Data Analysis

Affymetrix —  Developing systems to acquire, analyze and manage genetic info.
Agilent Technologies —   Provider of a range of microarrays for different organisms, manufacture the 2100 bioanalyzer.
Asper Biotechnology —   Manufacture coated microarray glass slides.
Axon Instruments —  Design and manufacture of instrumentation for genomics and proteomics.
BioDiscovery —   Providing software solutions for gene expression research.
BioMicro Systems — Providing the MAUI Hybridization system for active mixing of ultra low volumes during microarray hybridization.
BioRobotics —  Design, manufacture, and supply of automated solutions for molecular biology research.
BioSieve —  Provides microarray data analysis package on Java platform.
Cartesian Technologies —   Providing tools for microscale liquid handling and associated automation.
Clondiag Chip Technologies —  Imaging and LIMS software and technologies.
Clontech — Development and production of innovative biological products.
GeneData —  Providing computational solutions for analyisis of large quantities of data.
GeneLogic — Providing a data management platform for large-scale data analysis.
Genemachines — Developing machinery for genomics automation.
Gene Network Sciences — Developing dynamic computer models of living cells and next generation data-mining tools.
Genomic Solutions — Providing a variety of genomic research tools.
Genetix — Providing microarray printers, scanners, reagents and consumables.
Genotypic — A genomics and bioinformatics company, providing microarray products & services.
Genome Explorations Inc. — Providing Gene Expression analysis using the Affymetrix Platform.
Iobion Informatics LLC —   Microarray data management and analysis software.
LION Bioscience — Providing expression data analysis systems.
Molecular Dynamics —  Developing and manufacturing microarray systems.
Motorola Life Sciences — Developing system solutions for high-performance gene espression profiling.
MWG Biotech — Microarray provider of multiple whole genome arrays, custom arrays and other array products
Ocimum Biosolutions — Providing biotechnology software solutions, including Genowiz for micorarray data analysis and management.
Packard BioScience — Producing tools used in genomics and proteomics.
Perkin Elmer — Providing a list of various microarray products.
Rosetta Inpharmatics — Providers of bioinformatics solutions and gene expression analysis systems.
Scanalytics — Providing image analysis software for extracting and visualizing DNA microarray data.
Silicon Genetics — Providing genomic expression data analysis, visualization, mining, and storage products.
SSI Robotics — Robotic automation systems and instrument integration for life science related processes.
Superarray Bioscience — Developing pathway/application specific gene expression tools

Add more to this list…… !!!

September 3, 2009

WebArrayDB: A Platform for Microarray Data Analysis

Filed under: Bioinformatics,Microarray — Biointelligence: Education,Training & Consultancy Services @ 3:02 pm
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 Microarray Data Analysis

Cross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating, and analyzing large amounts of microarray data obtained from different array platforms.

An open source integrated microarray database and analysis suite, WebArrayDB (http://www.webarraydb.org), has been developed that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion, and allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student’s t-test, moderated t-tests, non-parametric tests, and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.
The software package is available for use on a public web server (http://www.webarraydb.org) or can be downloaded.

Check out WebArray at: http://www.webarraydb.org