Frontier Science Poster Presentations at the Society For Clinical Trials Annual Meeting
Frontier Science Amherst staff presented two posters at the Society For Clinical Trials 2018 annual meeting. A Unique Collaboration for a Data Coordinating Center outlines the INVESTED collaboration between the University of Wisconsin-Madison and the Frontier Science Data Management Center. Calculating Antiretroviral Drug Resistance: An Innovative Open-Source Tool showcases an antiretroviral drug resistance calculations tool developed at Frontier Science that uses customizable algorithms.
The INVESTED Collaboration
A Unique Collaboration for a Data Coordinating Center showcases a unique collaboration on a large cardiovascular study, INVESTED, with Dr. KyungMann Kim’s group at the University of Wisconsin-Madison and a Frontier Science Amherst data management group, led by Ken Wood, Project Manager.
Collaborating as one Data Coordinating Center on the project: INfluenza Vaccine to Effectively Stop cardioThoracic Events and Decompensated heart failure (INVESTED) (1 U01 HL130204), has provided several benefits to the research effort:
- Ideally staffing would lend itself for all aspects of data management to be done by one team at one institution/organization but given space and resource limitations — this does not always occur
- Sometimes partnerships outside one’s own institution are necessary to accomplish the end goal
- University of Wisconsin has a long-standing relationship with Frontier Science and Technology Research Foundation dating back to the 1970s
- Together both teams formed one stronger team to the benefit of the researchers that engage with them to answer important clinical questions
- Uniquely combines the strengths of the UW and Frontier Science in statistical methods for randomized controlled trials and data management and quality control/assurance.
The INVESTED Trial is designed to determine which of two formulations of influenza vaccine, the standard dose or an investigational higher dose, is more effective in reducing deaths and heart- or lung-related admissions to the hospital. Read more about the INVESTED Trial here.
The ASI Interpreter
Another poster presentation, Calculating Antiretroviral Drug Resistance: An Innovative Open-Source Tool, was led by Adina Stoica, who is the programmer manager of Frontier Science’s laboratory programming group. The Algorithm Specification Interface (ASI) Interpreter is an open source Java library that makes antiretroviral drug resistance calculations using customizable algorithms.
The ASI interpreter’s XML-based approach allows the rules for calculating resistance to be changed without altering program code. The rules used are easily readable by other scientists, enhancing transparency and replicability. The ASI Interpreter’s grammar is flexible enough to express an enormous variety of possible rules for calculating resistance or other results that can be calculated on the basis of viral mutations.
How The ASI Interpreter Works
The ASI Interpreter is a library, not a standalone application. It can be integrated with another program that needs to provide resistance results.
- The ASI Interpreter requires three inputs: an algorithm file, a gene region, and a list of mutations to evaluate.
- The algorithm file specifies the rules that are used to calculate resistance for each drug of interest. Each rule matches a condition (a set of mutation criteria) to an action. An action can be a score and resulting resistance level, a resistance level, or a comment.
- The ASI Interpreter takes the algorithm file that it is given and converts the rules into a logical structure to evaluate the given list of mutations. The logical structure takes the form of a tree in which each step in the detailed logic evaluating a rule is a node. The ASI Interpreter then systematically walks through the tree.
- Based on the type of actions specified in the rules, the interpreter can report a resistance level, a score (translated into a resistance level), and a set of comments.
Stephen Hart, Adel Ahmed and David Goss, also from Frontier Science, contributed to the presentation.
The 39th Annual Society For Clinical Trials Meeting was held May 20-23, 2018 in Portland, Oregon, USA. Frontier Science was a Gold level sponsor of the event.