{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2024/12/08/rich-l-apodaca.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/myaw4-dtg76", "url": "https://chem-bla-ics.linkedchemistry.info/2024/12/08/rich-l-apodaca.html", "title": "Richard L. Apodaca", "content_html": "

\"Screenshot\nIf you are into openscience chemistry or chemistry blogging, then you probably heard of\nRich Apodaca’s Depth-First blog. \nRich started blogging in 2006 but this is not\nhow I discovered his work originally. I know that we at least already had contact in 2005,\nbecause that is when he wrote about an integration between his Octet library and the Chemistry Development Kit\nin the CDK News (volume 2, issue 2),\nCDKTools: The CDK-Octet Bridge. In 2006 he reviewed our use of the Open Journal System for CDK News .

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But I did find we have been blogging about our work a lot. Searching for Rich\ngives false positives, but plenty of discussions of his work. At the same time, my name shows up multiple times \nin Depth-First too. Looking back at our shared history, we find, for example, Rich has blogged a lot about using the\nChemistry Development Kit in Ruby .

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Rich blogged about a lot of cheminformatics innovation. For example, \nin 2006 he was working on multi-atom bonding ,\nsuch as in ferrocene, something that is even today not routinely used in cheminformatics. I replied\nto that in this post.\nAnother thing he explored was embedding chemical graph notations in PNG images. In 2007 he\nwrote how to Never Draw the Same Molecule Twice: Image Metadata for Cheminformatics .\nThis was picked up by several others, including me with an implementation in JChemPaint.

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Another tool that I really liked was his Chempedia \nwhich collected “[f]ree chemical information resources created and reviewed by chemists”. One of the things it did\nwas link chemical names to chemical structures, e.g. for this compound .\nAnd because of the open license I was able to generate an RDF representation of Chempedia.\nThis resulted perhaps in one of my first online SPARQL endpoints.

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One and a half year ago he was confronted with health issues . Rich\nblogged openly about the months after that. Rereading this post is still hard, having seen cancer in action\non my mother. It turned out to be cancer, a brain tumor .\nJust this Thursday I attended a fascinating 2H NMR presentation, showing how much better\nwe got at recognizing tumors, but Rich’ MRI was obvious. He blogged for months on\nhis plan. Until the end of May \nthis year.

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Some weeks ago I received confirmation our fear; he passed away. Richard L. Apodaca was\nborn in 1968,\ncompleted his PhD at the University of Texas at Austin in 1996 on Studies in enantioselective catalysis:\n(1) a new class of chiral C₂-symmetric bisphenols; (2) Diorganotin dihalides (wikidata:Q131405461).\nRich published multiple papers in the field of medicinal chemistry (see his Scholia profile),\nwas very active in open science and held many patents.\nHis latest work was about Balsa: A Compact Line Notation Based on SMILES\n(see doi:10.26434/chemrxiv-2022-01ltp).

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The Depth-First blog has a CC-BY 2.0 license and perhaps Rogue Scholar \ncan archive it? It helps us remember Rich and his contributions to open science cheminformatics.

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References

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Apodaca, R. (2006). Changes. In Front Matter. Front Matter. https://doi.org/10.59350/xyp0f-9dt42 CrossRef Scholia
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Apodaca, R. (2006). Disruptive Innovation in Scientific Publishing: Free Journal Management Systems. In Front Matter. Front Matter. https://doi.org/10.59350/esgte-mv539 CrossRef Scholia
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Apodaca, R. (2006). Ferrocene and Beyond: A Solution to the Molecular Representation Problem. In Front Matter. Front Matter. https://doi.org/10.59350/pz3p6-fv247 CrossRef Scholia
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Apodaca, R. (2007). Never Draw the Same Molecule Twice: Image Metadata for Cheminformatics. In Front Matter. Front Matter. https://doi.org/10.59350/j026p-17z02 CrossRef Scholia
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Apodaca, R. (2007). Ruby CDK for Newbies. In Front Matter. Front Matter. https://doi.org/10.59350/50ebs-4zq55 CrossRef Scholia
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Apodaca, R. (2022). Balsa: A Compact Line Notation Based on SMILES. American Chemical Society (ACS). https://doi.org/10.26434/chemrxiv-2022-01ltp CrossRef Scholia
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Apodaca, R. (2023). Everyone Has a Plan. In Front Matter. Front Matter. https://doi.org/10.59350/mxqbw-ek659 CrossRef Scholia
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Apodaca, R. (2023). The Scary Stuff. In Front Matter. Front Matter. https://doi.org/10.59350/g29jj-d3m35 CrossRef Scholia
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Apodaca, R. (2024). Bridge to Nowhere. In Front Matter. Front Matter. https://doi.org/10.59350/6beed-gk067 CrossRef Scholia
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Apodaca, R. L. (2023). ER (Emergency Room). In Front Matter. Front Matter. https://doi.org/10.59350/5ct28-aaj63 CrossRef Scholia
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", "summary": "If you are into openscience chemistry or chemistry blogging, then you probably heard of Rich Apodaca’s Depth-First blog. Rich started blogging in 2006 but this is not how I discovered his work originally. I know that we at least already had contact in 2005, because that is when he wrote about an integration between his Octet library and the Chemistry Development Kit in the CDK News (volume 2, issue 2), CDKTools: The CDK-Octet Bridge. In 2006 he reviewed our use of the Open Journal System for CDK News .", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/depth_first.png", "date_published": "2024-12-08T00:00:00+00:00", "date_modified": "2025-02-22T00:00:00+00:00", "tags": ["openscience","cheminf"], "_references": [ { "url": "https://doi.org/10.26434/chemrxiv-2022-01ltp", "doi": "10.26434/chemrxiv-2022-01ltp" } , { "url": "https://doi.org/10.59350/xyp0f-9dt42", "doi": "10.59350/xyp0f-9dt42" } , { "url": "https://doi.org/10.59350/esgte-mv539", "doi": "10.59350/esgte-mv539" } , { "url": "https://doi.org/10.59350/50ebs-4zq55", "doi": "10.59350/50ebs-4zq55" } , { "url": "https://doi.org/10.59350/pz3p6-fv247", "doi": "10.59350/pz3p6-fv247" } , { "url": "https://doi.org/10.59350/j026p-17z02", "doi": "10.59350/j026p-17z02" } , { "url": "https://doi.org/10.59350/5ct28-aaj63", "doi": "10.59350/5ct28-aaj63" } , { "url": "https://doi.org/10.59350/g29jj-d3m35", "doi": "10.59350/g29jj-d3m35" } , { "url": "https://doi.org/10.59350/6beed-gk067", "doi": "10.59350/6beed-gk067" } , { "url": "https://doi.org/10.59350/mxqbw-ek659", "doi": "10.59350/mxqbw-ek659" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }