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Upgrade_Report_OpenChrom.md

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OpenChrom

Link to github issue trackter: #15

OpenChrom

• source code: https://github.com/OpenChrom
• OpenChrom version is using CDK 2.9 but is upgraded to CDK 2.10.
• what website to link to / how to acknowledge the previous source: https://openchrom.net or if applicable:
 OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data, Philip Wenig, Juergen Odermatt, BMC Bioinformatics; 2010, doi:10.1186/1471-2105-11-405

Code analysis

• OpenChrom uses API version3.10.0.
• to help find the maven modules that are dependencies:
    ○ org.openscience.cdk (2.10): 
        § compile: cdk-data, cdk-core, cdk-interfaces, cdk-render, cdk-renderbasic, cdk-standard, cdk-renderextra, cdk-extra, cdk-io, cdk-atomtype, cdk-ctab, cdk-ioformats, cdk-formula, cdk-dict, cdk-smiles, cdk-smarts, cdk-legacy, cdk-reaction, cdk-isomorphism, cdk-valencycheck, cdk-signature, cdk-charges, cdk-qsar:jar.
    ○ Javax (1.5.2:
        § compile: vecmath
    ○ gov.nist.math (1.0.3):
        § compile: jama
    ○ xom (1.3.9):
        § compile: xom
    ○ uk.ac.ebi.beam (1.3.8):
        § compile: beam-core, beam-func
    ○ com.github.gilleain.signatures (1.1):
        § compile: signatures
    ○ jgrapht (0.6.0):
        § jgrapht

• what functionality is being used: see list above.
    ○ OpenChrom is a program that can read and analyse chromatography and mass spectrometry data files. 
• record larger dependency eco-system (e.g. which tools depend on this tool)
    ○ OpenChrom
• how the code is being compile and executed
    ○ See the link to developers information on https://github.com/OpenChrom/openchrom/wiki/Quickstart
• how the code is tested

Upgrading tools

• what CDK API change affected the upgrade to 2.10. 
    ○ None.
• what testing results before and after the upgrade. 
    ○ None.
• who was involved? 
    ○ Matthias Mailänder & RvdPloeg

Reporting results

• where were the results announced? 
• how was the upgrade received/ used? 
    ○ cdk-2.10 is incorporated in the software.