Strand Life Sciences
Encyclopedia
Strand Life Sciences, formerly Strand Genomics, is a Bangalore
, India
-based in silico
technology company. Strand focuses in data mining
, predictive modeling, computational chemistry
, software engineering
, bioinformatics
, and research biology to develop software and services for life sciences research. Strand also offers custom solutions based on its intellectual property. In August 2007, Strand and Agilent Technologies, Inc. entered an agreement in which Strand develops and supports Agilent's GeneSpring software. In October 2010, Strand and Agilent renewed the agreement for Strand to expand the scope of Agilent's GeneSpring across multiple life sciences disciplines.
, Ramesh Hariharan, Swami Manohar
, and V. Vinay. It was registered as Strand Genomics, but was later renamed to Strand Life Sciences as it dealt with various other aspects of life sciences.
, next-generation sequencing, pre-clinical research, chemistry and healthcare.
.
, ABI
, and 454 Life Sciences
and supports fragment, paired-end and mate-pair library types. Aligned reads in SAM, BAM, BED or Eland formats can be imported into the tool.
Avadis NGS also allows users to perform quality control on the imported data and filter reads before the main analysis is performed. Version 1.1 of the tool supports three experiment types: ChIP-Seq, RNA-Seq
, and DNA-Seq. Gene
, transcript
, SNP, homology
, gene ontology
(GO), and other annotations needed for analysis can be downloaded directly from the Avadis NGS website.
Visualization tools, namely Genome Browser, Gene View, and Variant Support View, are a key aspect of the software. Other visualizations available with tool are scatter plot, MvA plot, profile plot, histogram
, heat map
, box and whisker plot, and Venn diagram
. Aided with visualizations, users a pictorial feel for statistical trends in the data.
Avadis NGS also provides access to organism-specific interaction databases containing relations between proteins, small molecules, enzymes, complexes, biological processes, molecular functions, and gene families. The two million interactions present in these databases can also be augmented by importing pathways in BioPAX
format from Reactome, Cancer Cell Map, etc. Gene lists generated by analysis steps can be used as the starting point for many pathway analysis operations.
Bangalore
Bengaluru , formerly called Bengaluru is the capital of the Indian state of Karnataka. Bangalore is nicknamed the Garden City and was once called a pensioner's paradise. Located on the Deccan Plateau in the south-eastern part of Karnataka, Bangalore is India's third most populous city and...
, India
India
India , officially the Republic of India , is a country in South Asia. It is the seventh-largest country by geographical area, the second-most populous country with over 1.2 billion people, and the most populous democracy in the world...
-based in silico
In silico
In silico is an expression used to mean "performed on computer or via computer simulation." The phrase was coined in 1989 as an analogy to the Latin phrases in vivo and in vitro which are commonly used in biology and refer to experiments done in living organisms and outside of living organisms,...
technology company. Strand focuses in data mining
Data mining
Data mining , a relatively young and interdisciplinary field of computer science is the process of discovering new patterns from large data sets involving methods at the intersection of artificial intelligence, machine learning, statistics and database systems...
, predictive modeling, computational chemistry
Computational chemistry
Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids...
, software engineering
Software engineering
Software Engineering is the application of a systematic, disciplined, quantifiable approach to the development, operation, and maintenance of software, and the study of these approaches; that is, the application of engineering to software...
, bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
, and research biology to develop software and services for life sciences research. Strand also offers custom solutions based on its intellectual property. In August 2007, Strand and Agilent Technologies, Inc. entered an agreement in which Strand develops and supports Agilent's GeneSpring software. In October 2010, Strand and Agilent renewed the agreement for Strand to expand the scope of Agilent's GeneSpring across multiple life sciences disciplines.
History
Strand Life Sciences was founded in October 2000 by Professors Vijay ChandruVijay Chandru
Vijay Chandru is an Indian entrepreneur. He is the founder and chairman of Strand Life Sciences.- Biography :Chandru received his bachelor degree from BITS Pilani and PhD from the MIT Sloan School of Management in 1982. He started his academic career in teaching and research in 1982. He served...
, Ramesh Hariharan, Swami Manohar
Swami Manohar
Swami Manohar is a co-founder and the CEO of PicoPeta Simputers Pvt. Ltd. After obtaining his PhD in Computer Science from Brown University he was a faculty at the University of North Carolina for two years and then was at the Indian Institute of Science , Bangalore, between 1990 to 2005...
, and V. Vinay. It was registered as Strand Genomics, but was later renamed to Strand Life Sciences as it dealt with various other aspects of life sciences.
Avadis
Avadis is a comprehensive data mining and visualization platform. It combines the power of scalable algorithms and dynamic interactive visualization. The platform was customized for various scientific domains like gene expressionGene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
, next-generation sequencing, pre-clinical research, chemistry and healthcare.
Sarchitect
Sarchitect is a platform for modeling and predicting drug-relevant properties of molecules in silicoIn silico
In silico is an expression used to mean "performed on computer or via computer simulation." The phrase was coined in 1989 as an analogy to the Latin phrases in vivo and in vitro which are commonly used in biology and refer to experiments done in living organisms and outside of living organisms,...
.
ArrayAssist
ArrayAssist was developed for Stratagene, Inc., based on the Avadis platform. The production was stopped after Stratagene was acquired by Agilent Technologies, Inc. in 2007.GeneSpring
GeneSpring GX (version 9.0.0 onwards), GeneSpring Workgroup (version 7.0.0 onwards), and Mass Profiler Pro are developed by Strand's R&D division in Bangalore.Avadis NGS
Avadis NGS is a software platform for next-generation sequencing data analysis. It can import pre-aligned read sequences from sequencing platforms like IlluminaIllumina
Illumina is the second album by Alisha's Attic to be released worldwide in 1998. Three tracks were released from it, these being "The Incidentals", "Wish I Were You" and "Barbarella". It peaked at #15 on the UK album chart...
, ABI
ABI
ABI is an acronym or abbreviation that may refer to:* Abilene Regional Airport , in Abilene, Texas, United States* Abitur* AbiWord* Acquired brain injury* Agencia Boliviana de Información, a Bolivian press agency...
, and 454 Life Sciences
454 Life Sciences
454 Life Sciences, is a biotechnology company based in Branford, Connecticut. It is a subsidiary of Roche, and specializes in high-throughput DNA sequencing.-History and Major Achievements:...
and supports fragment, paired-end and mate-pair library types. Aligned reads in SAM, BAM, BED or Eland formats can be imported into the tool.
Avadis NGS also allows users to perform quality control on the imported data and filter reads before the main analysis is performed. Version 1.1 of the tool supports three experiment types: ChIP-Seq, RNA-Seq
RNA-Seq
RNA-seq, also called "Whole Transcriptome Shotgun Sequencing" and dubbed "a revolutionary tool for transcriptomics", refers to the use of high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content, a technique that is quickly becoming...
, and DNA-Seq. Gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
, transcript
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
, SNP, homology
Homology
Homology may refer to:* Homology , analogy between human beliefs, practices or artifacts owing to genetic or historical connections* Homology , any characteristic of biological organisms that is derived from a common ancestor....
, gene ontology
Gene Ontology
The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
(GO), and other annotations needed for analysis can be downloaded directly from the Avadis NGS website.
- The ChIP-Seq analysis workflow allows users to identify enriched regions using three different peak finding algorithms - a simple sliding window based approach, MACS, and PICS. Depending on the experiment design, these regions could be transcription factorTranscription factorIn molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
binding sites, methylationMethylationIn the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...
sites, etc. Motifs present in the identified binding sites can be discovered using a parallel implementation of the GADEM algorithm. Entity lists containing the genes in the neighborhood of the binding regions can be created and used in downstream gene ontology, GSEA, pathway analysis.
- The RNA-Seq experiment workflow allows users to measure expression levels of known genes and transcripts. It also allows discovery of novel exons, genes and splice junction. The Genome BrowserGenome browserA genome browser is a graphical interface for display of information from a biological database for genomic data. Genome browsers enable researchers to visualize and browse entire genomes with annotated data including gene prediction and structure, proteins, expression, regulation, variation,...
in Avadis NGS enables users to validate the predictions by allowing viewing of the results in the context of annotations from multiple sources such as NCBINCBINCBI may refer to:* National Center for Biotechnology Information, part of the U.S. National Institutes of Health* National Coalition Building Institute, a U.S. non-profit training group...
, the UCSC Genome BrowserUCSC Genome BrowserThe University of California, Santa Cruz is an up-to-date source for genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations...
, and EnsemblEnsemblEnsembl is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project...
. Statistical tests, specifically designed to handling count based data, can be used for differential gene expression and alternative splicing analysis. A special "Gene View" visualization presents consolidated information about a gene and helps in the verifications of predictions.
- The DNA-Seq experiment workflow has links for SNP and structural variationStructural variationStructural variation is the variation in structure of an organism's chromosome. It consists of many kinds of variation in the genome of one species, and usually includes microscopic and submicroscopic types, such as deletions, duplications, copy-number variants, insertions, inversions and...
detection algorithms. The SNP prediction step finds homozygous and heterozygous SNPs and identifies overlaps with the provided dbSNP annotations. SNPs falling in genic regions are further analyzed and their effect on transcripts is described (similar to the Ensembl SNP Effect Prediction web-service). The structural variationStructural variationStructural variation is the variation in structure of an organism's chromosome. It consists of many kinds of variation in the genome of one species, and usually includes microscopic and submicroscopic types, such as deletions, duplications, copy-number variants, insertions, inversions and...
analysis algorithms identify homozygous and heterozygous indels, inversions and translocationTranslocationTranslocation may refer to:* Chromosomal translocation, in genetics* Translocation in plants, transport of food or pesticides through phloem or xylem* Protein translocation or protein targeting, a process in protein biosynthesis...
events.
Visualization tools, namely Genome Browser, Gene View, and Variant Support View, are a key aspect of the software. Other visualizations available with tool are scatter plot, MvA plot, profile plot, histogram
Histogram
In statistics, a histogram is a graphical representation showing a visual impression of the distribution of data. It is an estimate of the probability distribution of a continuous variable and was first introduced by Karl Pearson...
, heat map
Heat map
A heat map is a graphical representation of data where the values taken by a variable in a two-dimensional table are represented as colors. Fractal maps and tree maps both often use a similar system of color-coding to represent the values taken by a variable in a hierarchy...
, box and whisker plot, and Venn diagram
Venn diagram
Venn diagrams or set diagrams are diagrams that show all possible logical relations between a finite collection of sets . Venn diagrams were conceived around 1880 by John Venn...
. Aided with visualizations, users a pictorial feel for statistical trends in the data.
- Genome Browser in Avadis NGS is an interface to visualize data, results, and annotations associated with the genome in one place. Annotation data, such as cytobands, genes, transcripts, etc., as well as results from the analyses, such as Peak regions, SNPs, Gene Fusions, etc. can be superimposed. Users can drag and drop data into the browser and also perform search operations. To navigate in the Genome Browser, users can scroll, pan, and zoom. Users may also color, filter, and label data points of interest.
- Gene View is used to visualize individual genes and their transcripts. Users can see read coverage for known, as well as novel, exon partitions.
Avadis NGS also provides access to organism-specific interaction databases containing relations between proteins, small molecules, enzymes, complexes, biological processes, molecular functions, and gene families. The two million interactions present in these databases can also be augmented by importing pathways in BioPAX
BioPAX
BioPAX is a RDF/OWL-basedstandard language to represent biological pathwaysat the molecular and cellular level. Its major use is to facilitate the exchange of pathway data....
format from Reactome, Cancer Cell Map, etc. Gene lists generated by analysis steps can be used as the starting point for many pathway analysis operations.
Accolades
- Strand is a Red HerringRed herringA red herring is a deliberate attempt to divert attention.Red herring may refer to:* Red herring , the informal fallacy of presenting an argument that may in itself be valid, but does not address the issue in question....
"Asia 100 Private Company" for the years 2005 and 2010. - Deloitte Fast 50 India and Fast 500 Asia in 2009 and 2010.
- Strand Life Sciences named as "NASSCOM IT Innovator 2006" by NASSCOMNASSCOMThe National Association of Software and Services Companies of IT software and services related activities for use of both the software developers as well as interested companies overseas....
. It is one amongst seven Indian companies to be recognized by NASSCOM as IT Innovators in 2007. - Strand Life Sciences named as "Technology Pioneer 2007" by the World Economic ForumWorld Economic ForumThe World Economic Forum is a Swiss non-profit foundation, based in Cologny, Geneva, best known for its annual meeting in Davos, a mountain resort in Graubünden, in the eastern Alps region of Switzerland....
. - Strand has received the Frost & SullivanFrost & SullivanFrost & Sullivan, Inc. is an American firm which provides market research & analysis, growth strategy consulting and corporate training services. Its headquarters are located in San Antonio, Texas, with offices in over 20 countries across the world....
"Excellence in Technology Award 2005" for its technology platform Avadis. - 2003 Strand was nominated as a technology pioneer by the World Economic ForumWorld Economic ForumThe World Economic Forum is a Swiss non-profit foundation, based in Cologny, Geneva, best known for its annual meeting in Davos, a mountain resort in Graubünden, in the eastern Alps region of Switzerland....
for the year 2002. - Genome Technology Magazine nominated Strand as the top five most important companies in the category "Company of the Year 2002".