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Strand Life Sciences

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Strand Life Sciences Pvt. Ltd.
Company typePrivate
IndustrySoftware
Life Sciences
Healthcare
Founded2000
HeadquartersBangalore, Karnataka, India
Key people
Vijay Chandru , CEO
Ramesh Hariharan, CTO
Kas Subramanian, CSO
ProductsStrandAdvantage
Strand NGS
Heptox
Avadis
Websitewww.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[1] software which Agilent obtained through Silicon Genetics acquisition in August 2004.[2] In October 2010, Strand and Agilent renewed the agreement[3] 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[4] software which Agilent obtained through Silicon Genetics acquisition in August 2004.[5] In October 2010, Strand and Agilent renewed the agreement[6] 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[7] and 2010.[8]
  • Deloitte Fast 50 India and Fast 500 Asia in 2009 and 2010.
  • Strand Life Sciences named as "NASSCOM IT Innovator 2006" by NASSCOM.[9] 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.[10]
  • Strand has received the Frost & Sullivan "Excellence in Technology Award 2005"[11] 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

  1. ^ http://www.agilent.com/about/newsroom/presrel/2007/20aug-ca07049.html
  2. ^ http://www.biodevicesbiz.com/newsArticle.asp?nId=84896&cId=275
  3. ^ http://www.agilent.com/about/newsroom/presrel/2010/04oct-ca10065.html
  4. ^ "Agilent - Agilent Technologies and Strand Life Sciences Announce GeneSpring Development Agreement". agilent.com. 5 January 2017. Retrieved 22 February 2017.
  5. ^ "Agilent Technologies to Acquire Silicon Genetics, Leading Provider of Life Science Informatics". biodevicesbiz.com. Retrieved 22 February 2017.
  6. ^ "Agilent - Agilent Technologies and Strand Team Up to Advance Integrated Biology Software Systems". agilent.com. 4 October 2010. Retrieved 22 February 2017.
  7. ^ "Indecomm Global Services - partnerships@work" (PDF). indecommglobal.com. Retrieved 22 February 2017.
  8. ^ "www.herring100.com". herring100.com. Retrieved 22 February 2017.
  9. ^ http://www.nasscom.in/Nasscom/templates/NormalPage.aspx?id=50719
  10. ^ "Archived copy". Archived from the original on 23 October 2008. Retrieved 23 December 2008.{{cite web}}: CS1 maint: archived copy as title (link)
  11. ^ "Strand Genomics Walks away with the Frost & Sullivan Excellence in Technology Award for its avadis Platform". frost.com. Retrieved 22 February 2017.
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