Industry Posters


IP01 - Ion Reporter™: Software for Analysis of Semiconductor Sequencing Data
Scientific Area: Genetic Variation Analysis

Presenting author: Chrysanthi Ainali, Life Technologies, Germany

Additional authors:
Heinz Breu, Life Technologies, United States
Dumitru Brinza, Life Technologies, United States
Sowmi Utiramerur, Life Technologies, United States
Yuandan Lou, Life Technologies, United States
Alex Joyner, Life Technologies, United States
Brijesh Krishnaswami, Life Technologies, United States
Jing Zhai, Life Technologies, United States
Jonathan Mangion, Life Technologies, United States
Fiona Hyland, Life Technologies, United States
Ellen Beasley, Life Technologies, United States


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Ion Reporter™ Software is a hosted suite of informatics tools that streamlines and simplifies analysis, annotation, and archiving of semiconductor sequencing data. Designed specifically for researchers performing routine sequencing assays by automating the variant analysis bioinformatics pipeline, Ion Reporter™ Software detects variants and connects them with public annotations, allowing faster biological assessment. The workflow steps mirror the typical role-based sample processing workflow used in production labs. The software provides functionality for germline and low frequency variant calling in single samples, tumor and matched normal paired samples to identify somatic variants based on integrated evidence from matched tumor and normal samples, as well trio analysis. Different analysis modules used in the various workflows include alignment, mapping statistics, on and off target statistics, SNP and INDEL calling. The Tumor/Normal algorithm calls variants in the tumor sample, analyzing reads from the normal sample to remove variants with elevated background at the tumor variant position. The Tumor/Normal module was run on an 80:20 mixture of two HapMap samples (simulating low frequency somatic variants), and on a variety of real cancer samples. Ion Reporter Software supports family analysis with an algorithm for inference of inherited disease, which was used to analyze a HapMap trio on both the Ion AmpliSeq™ Inherited Disease Panel and with Ion TargetSeq Exome Kit™ sequencing runs of the full trio on the Ion PI™ chip. Ion Reporter™ Software provides an optimal solution for analysis of semiconductor sequencing data, as well as integration with third party software for case-control or pathway analyses.

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IP02 - Extending the BioXM Knowledge Management Platform to support sequence-centric applications for the Bioinformatics and Synthetic Biology domain
Scientific Area: Computational aspects

Presenting author: Verena Schuetz, Biomax Informatics AG, Germany

Additional authors:
Sebastian Toepel, Biomax Informatics AG, Germany
Hilly Menke, DSM, Netherlands
Renger Jellema, DSM, Netherlands
Marco de Groot, DSM, Netherlands
Hans Roubos, DSM, Netherlands
Sascha Losko, Biomax Informatics AG, Netherlands


Presentation Overview: Show/Hide
The BioXM™ platform of Biomax is a highly flexible, configurable and integrative data and knowledge management system. Its generalizing approach enables semantic modeling of domain-specific knowledge and allows for combining user-relevant results with publicly available knowledge from external databases. Due to easy and fast configuration customer-tailored applications range from pharmaceutical and clinical research, biobanking, next-generation sequencing, sequence analysis, pathway analysis, literature mining, systems biology to comparative genomics.

Together with DSM we have extended the BioXM platform to the field of synthetic biology, which aims at exploiting engineering principles of abstraction and standardization to design novel complex biological systems. BioXM now provides an infrastructure for sequence-centered applications easily accessible through a user-friendly, configurable Wiki platform. It serves as a repository for standard biological parts such as promoters, ORFs or terminators that can be visually assembled into constructs following a set of design specification rules to ensure correctness. To account for context dependency as an inherent characteristic of biological systems, a key advantage is that constructs can be characterized by wet lab information enabling collaborative feedback that gives valuable knowledge for future construct design.

Together with the connection to external databases such as Pubmed and Uniprot and integration of public or proprietary sequence analysis tools like EMBOSS, codon optimization algorithms, BLAST, ClustalW as well as the possibility to query the system for relevant biological and functional information, this novel extension of the BioXM platform will streamline strain optimization and demonstrates its unique capability to meet the needs of the life sciences industry.

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