This document discusses software testing in the life sciences domain. It notes that life sciences data involves large volumes of data that can be represented in different ways. While there are engineering issues to consider when testing life sciences software, the principles of testing do not differ. Examples are given of types of life sciences software like genome browsers and molecular viewers. The document provides suggestions for test data sources and discusses tools and languages commonly used for automated testing of life sciences software like Java, Selenium, and Python. It also highlights some challenges in automating the testing of things like canvas elements and 3D models. Links are provided to open source projects and demos from EPAM as examples.

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ADVANCED VISUAL
ANALYSIS OF GENOMIC
VARIATIONS USING
NGB
August, 2017
FEATURES OF SOFTWARE
TESTING IN LIFE SCIENCES
DOMAIN
Vladimir Poliakov,
Software Test Automation
Engineer
March, 2018

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• Big volume of data
• Different representation of the same data
• New specific feature
• Specific languages
Problems

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New Generation Sequencing

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Big volume of data

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Different representation of the same data
This is the same data for biologist.

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Different representation of the same data

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New features

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Specific languages and code representation

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How to test life sciences software?
• Engineering issues (e.g. test script language)
• No principals different in testing
• You can find analogs

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• * Genome browsers:
– IGV
– Jbrowse
– Ugene
• Molecular viewers :
• VMD
• PyMol
You can find analogs

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• You have base knowledge in biology and chemistry
• Biology it is fun and simple
• BA can teach you
Specific knowledge of domain

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• PDB bank http://www.rcsb.org
• Gene files and other https://www.ensembl.org
• Stack Overflow for bioinformatics https://www.biostars.org
Test data

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• Tools and languages:
– Java
– Selenium
– JDI
– CoreJS
– Python
– Bash
– Git+TravisCI+Saucelabs
Automated testing
Git commit Travis build Tests on SL

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Automatization
• Tables and filters (easy to test)
• Menus

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Automatization overview
• Set WDL script in codemirror element
• Get SVG content
• Convert SVG to PNG (JS)
• Compare images

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Automatization overview
• Find canvas element
• Get content use JQuery
• Convert Base64 string to PNG
• Compare images

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Problems in automatization
• Tips for canvas elements
• Picture validation
• Regression testing of 3D models

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• Genome browser sources: https://github.com/epam/NGB
• Genome browser demo: http://ngb.opensource.epam.com/catgenome/#/
• Molecular viewer sources: https://github.com/epam/miew
• Molecular viewer demo: http://miew.opensource.epam.com/v0.6.0/#/
• Pipeline builder sources: https://github.com/epam/pipeline-builder
• Pipeline builder demo: http://pb.opensource.epam.com/
Sources and Demo.