When it comes to recruiting beta testers for Strand Life Science’s upcoming next-generation sequence analysis software, Thon de Boer, director of software product management for Strand, says, “the more, the merrier.”
Strand, based in India and the US, recently issued a call for researchers to beta test its newest software offering and provide feedback, which will be integrated into Avadis NGS 1.0, scheduled for release later this year.
“It’s not a beta [test] where [researchers] are just trying things and can provide feedback if they feel like it,” de Boer told Bioinform. “We are going to be very hands-on with the beta customer, calling them and asking them questions and really finding the issues.”
De Boer said that the company began beta testing Avadis NGS on Sept. 2 and that so far more than ten groups have signed on to test the software. Strand will accept beta testers until Sept 24 when the call closes and is planning to release the first version of the software on Oct. 4.
Avadis NGS is being developed to analyze next-generation sequencing data from ChIP- and RNA-sequencing and DNA variation experiments.
In addition to the standard peak finding and motif detection applications, de Boer says that the software incorporates tools that fit with the company’s goal of providing “biological answers” for customers.
“Our customers are biologists that have a biological question [such as], 'What’s the cause of this particular disease?'” he said. “We really want to get them to that answer quickly.”
The software is built on the company’s Avadis development platform, which forms the basis for all the products that Strand has developed over the last eight years.
For example, GeneSpring GX, which Strand developed in partnership with Agilent Technologies, was built on the Avadis platform. The software lets users visualize and analyze gene expression data.
According to de Boer, Avadis NGS will take the capabilities available in GeneSpring GX a step further by focusing "on the specific problems that NGS platforms have provided.”
One such problem pertains to access to annotation data which is often contained in several different databases. To get around this drawback, De Boer said that Strand provides pre-packaged annotation data for Avadis NGS users "that can be directly downloaded in the tool itself without having to leave the tool."
In addition, de Boer said that Avadis NGS lets researchers analyze large quantities of sample data on desktop computers noting that most researchers don't have access to large compute clusters or cloud computing infrastructure.
Cloaking Complexity in Simplicity
When Avadis NGS 1.0 goes on the market, it will be a “generic” desktop application capable of running on Windows, Mac, Linux systems.
The software will take SAM or BAM files containing previously aligned sequence data and then “hide the complexity” for users by passing the data directly through the relevant RNA-, ChIP-seq, and DNA variation workflows.
“What we have noticed is that the bottleneck in analyzing NGS data has been in the complexity of the tools that have been available,” de Boer said. “There are many open source tools available but you need to be an expert. We focus on the biologists [who] aren’t necessarily experts in bioinformatics but they just want to get their answer.”
“So, for ChIP-seq [experiments], we only show you the tools and the algorithms that are relevant for the ChIP-seq experiments,” he continued. “[The software] doesn’t bother you with any of the other steps like ANOVA, for instance, which isn’t relevant for ChIP-seq.”
To analyze ChIP-seq data, Avadis NGS uses the MACS (model-based analysis of ChIP-seq) and PICS (probabilistic inference of ChIP-seq) algorithms to locate peaks where transcription factors bind, and also performs a Gene Ontology analysis to find commonalities among genes in the same region of the genome. It provides a genome browser that gives a complete picture of the genome, including the individual aligned reads, as well as a visual biological pathway that lets users identify connections among the genes.
De Boer noted that having a “strong statistical analysis” tool is only part of the equation. “What you really need is all these metadata around the sequence,” he said.
To address that issue, the software brings together data from public databases from the National Center for Biotechnology Information, the European Bioinformaitics Institute, and elsewhere in order to provide a “one stop shop for [researchers] to get all the data that is relevant for the analysis that they are doing”
For the version 1.0 release, Avadis will be an independent application but de Boer said that Strand plans to develop a version of the software that will be integrated with Agilent’s GeneSpring and provide a “seamless solution” for going from “arrays all the way down to using next-gen sequencing data."
De Boer did not say when the integrated version of the software would be released but he did say it would be “very soon” after the release of Avadis 1.0.
Getting the Word Out
De Boer said that Avadis NGS is already being tested by some of Strand’s collaborators but he declined to mention their names. He did say, however, the company wants the product to be tested by a much wider audience.
To that end, one resource that the company is using to locate potential beta testers is the SEQanswers sequencing forum. De Boer said that the medium was a “logical extension” for Strand to recruit researchers for the test because it’s where a lot of the company’s “customer base goes” to ask and respond to each other’s questions. Since the call went out, de Boer said that the company has already identified some potential testers.
The company is still working out how much Avadis NGS will cost so de Boer declined to comment on the issue but he did say that the software would be “competitively priced.”
“We really think that we’ve got a unique piece of software but we are not the only ones so we want to make sure that we get it in as many hands as we can,” he said.
Indeed, the company will be rolling out its software amid a fiercely competitive market that is growing ever more crowded. Established bioinformatics firms such as CLC Bio, Geospiza, GenomeQuest, DNAStar, and SoftGenetics have had NGS analysis products on the market for several years now. In addition, new players such as DNANexus and Biomatters are moving onto the scene with new bioinformatics products and services targeted at the NGS market.
But de Boer said that one of the main selling points for Strand's software — and a key feature of the company’s marketing strategy — is that many tools such as Partek's next gen sequence analysis software, require some expertise in computer science, while Avadis NGS is easy to use.
We provide an application that is easier to use for the biologist who is a non-expert, unlike some of the competitive offerings," he said. “Some of the tools that are out there are still very much focused on the experts who want to have all the latest algorithms and all the flexibility in the world, Avadis NGS provides 'NGS analysis for the rest of us'."
To develop Avadis NGS, de Boer said, Strand researchers pored through the literature to identify the algorithms "that researchers have found the most useful or algorithms that people have been using the most.”
In addition to Avadis NGS, de Boer said the company is also developing a system for creating biological models that is being used to develop an in silico model of a liver. He said that the company is currently working on validating the model using real data and at this time does not have a specific release date.
Currently Strand has about 150 employees in offices in Bangalore, India, and San Francisco, California and de Boer said it plans to “expand its footprint” in Europe.