Rancho Biosciences said this week that it has joined the Orion Bionetworks alliance — a network of researchers, patient advocates, and data specialists that study new diagnostics, treatments, and cures for brain disorders.

Joining the network is an important step for San Diego, Calif.-based Rancho as it attempts to build is business. The company, which launched officially late last year, provides fee-based bioinformatics analysis, IT infrastructure, knowledge representation, and data-curation services to pharmaceutical companies, non-profit foundations, and academics.

“It lets people know what we are doing for Orion and what we can do for other groups” and that “we have capacity to take on many more projects,” Rancho CEO Julie Bryant told BioInform.

Under the terms of its agreement with Orion, Rancho will provide data curation, ontologies, and vocabularies around TranSMART — an open source knowledge management platform that is composed of a federated data warehouse and analysis software. It will also offer genomic and clinical data analysis and help create disease pathway models that incorporate different kinds of data.

These services will support Orion’s multiple sclerosis project, a two-phase effort that among other things aims to understand the genetic or environmental factors of disease progression; discover the underlying reasons for varying treatment responses; and identify targets and pathways that could be used to develop more personalized therapies.

In the first phase, the alliance aims to build a predictive model of MS based on demographic information, brain imaging data, information on disease course and clinical response to treatments, and changes in gene activity collected before and after treatment from 7,000 people living with MS. The data comes from the Comprehensive Longitudinal Investigation of MS at the Brigham and Women’s Hospital, or CLIMB, dataset; the Accelerated Cure Project; and PatientsLikeMe.

The second phase will see the expansion of Orion’s MS database to include brain scans, biomarkers, and phenotypic data from clinical study centers and prospective studies. These data will be used to build a second set of simulations aimed at identifying primary disease mechanisms in MS.

The financial details of the partnership are not being disclosed.

Rancho’s commercial offerings include curation services; analysis of next-generation sequencing, gene expression, proteomics, metabolomics, and other kinds of omics data; and information technology services such as data integration, software development, database administration, and application building. The company makes use of open source tools such as the R programming language and data from public resources such as the Gene Ontology, The Cancer Genome Atlas, and the Allen Brain Atlas.

It also offers access to a hosted version of TranSMART or it can install the platform locally for customers who prefer to have an in-house system. TranSMART clients can also avail themselves of the company’s data curation, knowledge representation, and bioinformatics services for the platform as well as IT services such as custom dashboards and workflows and third-party tool integrations.

Bryant told BioInform that her firm charges on a per-project basis for its services and that the costs vary depending on the length and nature of the project. The company currently has nine employees and six consultants with expertise in areas such as IT, systems biology, quantum chemistry, and biochemistry. It is looking to hire additional bioinformaticians and a data curator.

“We bring to the table special expertise that we’ve all grown over the years,” she said. “I think there is a lot of competition … but the majority of us have worked together very successfully at previous companies and we’re rebuilding it again here.”

What also sets Rancho apart from competing service providers, Bryant said, is that it intends to make some fruits of its projects open to the community so that others can benefit from its work and to reduce the time and resources wasted on repeated research.

“When we are working on some projects, maybe it’s building a certain ontology or … manually curating some content or information or building some piece of software, we want to put that in the public domain,” she said. “I don’t know any … commercial company wanting to put things in the public domain. They usually build them and then resell.”

By Uduak Grace Thomas

Genomeweb June 28, 2013