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{{Short description|Indian technology company}}
{{Use dmy dates|date=September 2016}}
{{Use Indian English|date=September 2016}}
{{Infobox company |
name = Strand Life Sciences Pvt. Ltd.|
logo = strandlogo.png|
type = [[Private Company|Private]] |
foundation = 2000 |
location = [[Bangalore]], [[Karnataka]], [[India]]|
key_people = [[Vijay Chandru]] , CEO Ramesh Hariharan, CTO Kas Subramanian, CSO|
industry = [[Software]] [[Life Sciences]] [[Healthcare]] |
products = StrandAdvantage Strand NGS Heptox Avadis|
homepage = [http://www.strandls.com/ www.strandls.com]
}}
'''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<ref>http://www.agilent.com/about/newsroom/presrel/2007/20aug-ca07049.html</ref> software which Agilent obtained through Silicon Genetics acquisition in August 2004.<ref>http://www.biodevicesbiz.com/newsArticle.asp?nId=84896&cId=275</ref> In October 2010, Strand and Agilent renewed the agreement<ref>http://www.agilent.com/about/newsroom/presrel/2010/04oct-ca10065.html</ref> 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<ref>{{cite web|url=http://www.agilent.com/about/newsroom/presrel/2007/20aug-ca07049.html|title=Agilent - Agilent Technologies and Strand Life Sciences Announce GeneSpring Development Agreement|date=5 January 2017|work=agilent.com|accessdate=22 February 2017}}</ref> software which Agilent obtained through Silicon Genetics acquisition in August 2004.<ref>{{cite web|url=http://www.biodevicesbiz.com/newsArticle.asp?nId=84896&cId=275|title=Agilent Technologies to Acquire Silicon Genetics, Leading Provider of Life Science Informatics|work=biodevicesbiz.com|accessdate=22 February 2017}}</ref> In October 2010, Strand and Agilent renewed the agreement<ref>{{cite web|url=http://www.agilent.com/about/newsroom/presrel/2010/04oct-ca10065.html|title=Agilent - Agilent Technologies and Strand Team Up to Advance Integrated Biology Software Systems|date=4 October 2010|work=agilent.com|accessdate=22 February 2017}}</ref> for Strand to expand the scope of Agilent's GeneSpring across multiple life sciences disciplines.

==Software==

===Strand NGS (formerly Avadis NGS)===
[http://www.strand-ngs.com/ Strand NGS] is a software platform for [[next-generation sequencing]] data analysis. It can import raw read sequences from sequencing platforms like [[Illumina (company)|Illumina]], [[Ion Torrent]], [[Pacific Biosciences|PacBio]], [[Applied Biosystems|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 [[Chromosomal translocation|translocation]]s.

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]], [[transcription (genetics)|transcript]], [[Single-nucleotide polymorphism|SNP]], [[Homology (biology)|homology]], [[gene ontology]] (GO), and other annotations needed for analysis can be downloaded directly from within Strand NGS [http://www.strand-ngs.com/ 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 [[National Center for Biotechnology Information|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 [[Single-nucleotide polymorphism|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 [[Chromosomal translocation|translocation]] events. In addition, [[Copy number variation|Copy Number Variation]]s 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 (magazine)|Red Herring]] "Asia 100 Private Company" for the years 2005<ref>{{cite web|url=http://www.indecommglobal.com/downloads/RH_sep_05_05.pdf|title=Indecomm Global Services - partnerships@work|work=indecommglobal.com|accessdate=22 February 2017}}</ref> and 2010.<ref>{{cite web|url=http://www.herring100.com/rha2010/winners/2010winners.html|title=www.herring100.com|work=herring100.com|accessdate=22 February 2017}}</ref>
* [[Deloitte]] Fast 50 India and Fast 500 Asia in 2009 and 2010.
* Strand Life Sciences named as "NASSCOM IT Innovator 2006" by [[NASSCOM]].<ref>http://www.nasscom.in/Nasscom/templates/NormalPage.aspx?id=50719</ref> 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]].<ref>{{cite web |url=http://www.weforum.org/en/Communities/Technology%20Pioneers/SelectedTechPioneers/TechnologyPioneers2007/index.htm |title=Archived copy |accessdate=2008-12-23 |url-status=dead |archiveurl=https://web.archive.org/web/20081023044137/http://www.weforum.org/en/Communities/Technology%20Pioneers/SelectedTechPioneers/TechnologyPioneers2007/index.htm |archivedate=23 October 2008 |df=dmy-all }}</ref>
* Strand has received the [[Frost & Sullivan]] "Excellence in Technology Award 2005"<ref>{{cite web|url=http://www.frost.com/prod/servlet/press-release.pag?docid=44422323|title=Strand Genomics Walks away with the Frost & Sullivan Excellence in Technology Award for its avadis Platform|work=frost.com|accessdate=22 February 2017}}</ref> 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".

== References ==
{{Reflist|30em}}

==External links==
*[http://www.strandls.com/ Strand Life Sciences]

{{Authority control}}

[[Category:Biotechnology companies of India]]
[[Category:Software companies of India]]
[[Category:Biotechnology companies established in 2000]]
[[Category:Information technology companies of Bangalore]]
[[Category:Privately held companies of India]]
[[Category:2000 establishments in Karnataka]]

Strand Life Sciences - Revision history

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