From Bench to Bedside: A View on Bioinformatics Pipelines
Although sequencing technology has become widely available in recent years, the steps in bioinformatics pipelines are time-consuming and barely standardized. New tools to improve individual steps in a pipeline are frequently published and configurations can be quickly adapted to use new versions. We performed case studies with a representative set of pipeline management tools using the GEP-R pipeline, and a qualitative study of different software packages covering relevant classes of software tools. We use a software toolset of R environment, Docker, KNIME, and BPEL to review our first aim of technical and organizational challenges. We propose snapshotting, documentation management, and a hybrid approach for our second aim of approaches to reproducibility. In order to have fully reproducible results derived from raw data, we think that it is necessary to archive biomedical analysis pipelines and their necessary software components.
Medical Informatics Computational Biology Software
Blanca Flores Dirk Hose Anja Seckinger Petra Knaup Matthias Ganzinger
Institute of Medical Biometry and Informatics,Heidelberg University,Heidelberg,Germany Department of Internal Medicine,Heidelberg University Hospital,Heidelberg,Germany
国际会议
第十六届世界医药健康信息学大会((MEDINFO2017)、第二届世界医药健康信息学华语论坛(WCHIS 2017)、第15届全国医药信息学大会(CMIA 2017)
苏州
英文
375-378
2017-08-21（万方平台首次上网日期，不代表论文的发表时间）