Skip to main content

Swedish Bioinformatics Company Hopes to Ease the Pain of Analyzing Gene Expression Data

STOCKHOLM, July 5 – One of the leading complaints among scientific researchers is that current software solutions do not ensure the ability to make heads and tails of the massive amounts of gene expression data they generate.

Now, a Swedish company is hoping that its soon-to-be-released software will help researchers to eliminate this bottleneck.

Visual Bioinformatics of Stockholm is currently gearing up for the fall release of GeneWeaver, a bioinformatics tool designed to do away with awkward multi-screen formats by providing researchers with a way to cluster the data into one 2-D matrix that looks like a microarray.

“The chip concept allows you to group spots together based on any criteria and it gives you an overview without having to jump between screens,” said Tim Wood, senior project manager at Visual Bioinformatics.

While many people have questioned the long-term viability for bioinformatics companies, Wood said that GeneWeaver’s novel approach to organizing and analyzing gene expression data should help the company to find its market niche.

The program can be used for data coming from most types of chips and bioarrays, including sequence-based and hybridization-based tools, and it can also incorporate data that doesn’t come off of a chip, Wood said.

In addition, GeneWeaver allows users to hot-link to other external or proprietary data. All of the data can then be grouped based on a number of different parameters, such as discreet expression patterns, sequence homology, and particular pathways of interest. The software also contains algorithms to normalize the data and conduct  pair wise comparisons.

“Basically its very flexible,” said Wood, adding that the data structure is based on Oracle while the software is Java-based.

Wood said that Visual Bioinfomatics’ closest competitor was Spotfire, although he argued that the Swedish company’s smaller size would make it more agile and responsive to changes in genomics.  

Visual Bioinformatics was founded last year by researchers from Sweden’s Karolinska Institutet and the Royal Institute of Technology. To date, the company of 15 has raised “several million dollars” from Sweden's HealthCap Ventures, Karolinska Institutet, and KTH Holding.

The company is planning to hire another five people by the end of the year, and Wood noted that they have enough money to achieve this goal without raising any additional funds. The company has not yet finalized the location of the beta sites or the price  GeneWeaver will sell for.

In addition to GeneWeaver, Visual Bioinformatics is also currently working on SNPWeaver, a software solution similar to their flagship product, but designed, as the name states, for analyzing SNPs. After that the company is hoping to create a software tool to help analyze proteins. Visual Bioinfromatics is in ongoing discussions with Swedish proteomics company Affibody to develop proteomics tools.

Eventually, however, Wood said that the company, which is heavily focused on doing in silico biology, would have to look beyond providing tools to offer value-added goods to potential customers. 

“In the long-term developing tools just isn’t enough – you need to provide data,” Wood said.

The Scan

US Supports Patent Waivers

NPR reports that the Biden Administration has announced its support for waiving intellectual property protections for SARS-CoV-2 vaccines.

Vaccines Versus Variants

Two studies find the Pfizer-BioNTech SARS-CoV-2 vaccine to be effective against viral variants, and Moderna reports on booster shots to combat variants.

CRISPR for What Ails You

The Wall Street Journal writes that CRISPR-based therapies could someday be used to treat common conditions like heart attacks.

Nature Papers Review Integration of Single-Cell Assay Data, Present Approach to Detect Rare Variants

In Nature this week: review of ways to integrate data from single-cell assays, and more.