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Upgrade_Report_SmartCyp.md

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SMARTCyp

Link to github issue trackter: #22

SMARTCyp

• source code: http://smartcyp2.sund.ku.dk/download.php
• SMARTCyp version 2.4.2 is using CDK 2 is upgraded to CDK 2.9.
• what website to link to / how to acknowledge the previous source:  or if applicable:

SMARTCyp 2.4.2
P. Rydberg, D. E. Gloriam, J. Zaretzki, C. Breneman and L. Olsen, ACS Med. Chem. Lett., 2010, 1, 96-100 , P. Rydberg, D. E. Gloriam and L. Olsen, Bioinformatics, 2010, 26, 2988-2989, P. Rydberg and L. Olsen, ACS Med. Chem. Lett., 2012, 3, 69-73, P. Rydberg and L. Olsen, ChemMedChem, 2012, 7, 1202-1209, P. Rydberg et al., Angew. Chem, Int. Ed. 2013, 52, 993-997 and P. Rydberg et al., Mol. Pharmaceutics 2013, 10, 1216-1223.

SMARTCyp 3.0
Lars Olsen, Marco Montefiori, Khanhvi Phuc Tran, Flemming Steen Jørgensen, SMARTCyp 3.0: enhanced cytochrome P450 site-of-metabolism prediction server, Bioinformatics, Volume 35, Issue 17, September 2019, Pages 3174–3175,  https://doi.org/10.1093/bioinformatics/btz037

Code analysis

• SmartCyp 2.4.2 uses
• to help find the maven modules that are dependencies:
    ○ org.openscience.cdk (2.9):
    ○ org.openscience.cdk (2.2):
        § Compile: 
            □ cdk-data: cdk-interfaces, cdk-core.
            □ cdk-renderbasic (cdk-standard, cdk-render), cdk-renderawt, cdk-renderextra
            □ cdk-extra: cdk-io, cdk-atomtype, cdk-ctab:jar, cdk-ioformats, cdk-valencycheck, cdk-formula, cdk-dict, cdk-smiles.
            □ cdk-sdg.
            □ cdk-smarts: cdk-isomorphism.
            □ cdk-legacy: cdk-signature, cdk-qsar, cdk-charges, cdk-reaction.

• 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 incorperated in the software.