Strand Life Sciences, formerly Strand Genomics, is a Bengaluru, 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 which Agilent obtained through Silicon
Genetics acquisition in August 2004.
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 Chandru, 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.
In August 2007, Strand and Agilent Technologies, Inc. entered an agreement in which Strand
develops and supports Agilent's GeneSpring software which Agilent obtained through Silicon
Genetics acquisition in August 2004.
In October 2010, Strand and Agilent renewed the agreement for Strand to expand the scope
of Agilent's GeneSpring across multiple life sciences disciplines.
== Software ==
=== Strand NGS (formerly Avadis NGS) ===
Strand NGS is a software platform for next-generation sequencing data analysis.
It can import raw read sequences from sequencing platforms like Illumina, Ion Torrent, PacBio,
ABI, and 454 Life Sciences and supports fragment, single-end, paired-end, mate-paired, directional
single/ paired end library types.
Raw reads in formats FASTA, FASTQ, SAM, BAM, Unaligned BAM, BED, Counts data, VCF, VAL,
or Eland formats can be imported into the tool.
In addition, perform split read alignment for detecting long InDels and translocations.
Strand NGS also allows users to perform quality control on the imported data and filter reads
before the main analysis is performed.
Version 2.6 of the tool supports six experiment types: ChIP-Seq, RNA-Seq, small RNA, Methyl-Seq,
MeDIP-Seq and DNA-Seq.
Gene, transcript, SNP, homology, gene ontology (GO), and other annotations needed for analysis
can be downloaded directly from within Strand 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 factor binding
sites, methylation 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 Gene Set Enrichment Analysis (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 Browser in Strand NGS enables users to validate the predictions by allowing viewing
of the results in the context of annotations from multiple sources such as NCBI, the UCSC
Genome Browser, and Ensembl.
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 variation 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 variation analysis algorithms identify homozygous and heterozygous InDels,
inversions and translocation events.
In addition, Copy Number Variations can be detected using tumor-normal pairs.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.
Genome Browser in Strand 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.Strand 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 GPML format (WikiPathways), XML format (BioCyc), 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.
=== 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 === 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 expression, next-generation
sequencing, pre-clinical research, chemistry and healthcare.
=== Sarchitect === Sarchitect is a platform for modeling and
predicting drug-relevant properties of molecules in silico.
=== 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.
== Accolades == Strand is a Red Herring "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 NASSCOM.
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 Forum.
Strand has received the Frost & Sullivan "Excellence in Technology Award 2005" for its technology
platform Avadis. 2003 Strand was nominated as a technology
pioneer by the World Economic Forum for the year 2002.
Genome Technology Magazine nominated Strand as the top five most important companies in
the category "Company of the Year 2002