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The following is kept as an archive, but probably won't be updated regularly.

Welcome to the Indiana Cheminformatics Education Portal (ICEP). is a repository of freely accessible cheminformatics educational materials maintained by David Wild, director of the Indiana University Cheminformatics Program. The purpose of this repository is to broaden education in cheminformatics, an effort that includes several other initiatives including an innovative cheminformatics distance education program, a Graduate Certificate in Chemical Informatics from Indiana University, a low cost cheminformatics self-study guide, and a collaboration with Open Source Drug Discovery for sharing of cheminformatics educational materials. ICEP includes free introductory learning materials, videos, and news, social media, and latest journal articles relating to cheminformatics.


New!!

We now are running a free online introductory cheminformatics course - it's not too late to join.

ICEP's wiki-based introductory cheminformatics learning materials


The following introductory topics are adapted from materials that we use in our I571 Chemical Information Technology class, which serves as our introductory cheminformatics course at Indiana University. These themes are developed further in the Introducing Cheminformatics eBook


Free short tutorial videos





Introducing Cheminformatics eBook now available for $25 - also available in library and company versions



external image icbookcover.jpg?height=200&width=154New eBook! - Introducing Cheminformatics: an intensive self-study guide.
This Lulu PDF eBook gives an intensive introduction to cheminformatics, including the history of the field, representing 2D and 3D chemical structures on computer, storing and using databases of chemical and related biological information, handling chemical information on the web and in the scholarly literature, and giving an overview of some advanced topics such as clustering and diversity, QSAR and predictive modeling, 3D alignment and docking, and software toolkits cheminformatics software. It is aimed at life scientists and computer scientists in both industry and academia who need a rapid, flexible introduction to this field, and comes as a regular PDF. It is available in an individual version for $25, or in versions that can be used in an academic library system or company-wide. For more information, check out the eBook on Lulu.


Other learning resources




Cheminformatics news, blogs and social media





      chem-bla-ics
      • new paper: "A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury" by Egon Willighagen Jul 5, 2017
        Figure from the article. CC-BY.One of the projects I worked on at Karolinska Institutet with Prof. Grafström was the idea of combining transcriptomics data with dose-response data. Because we wanted to know if there was a relation betwee...
      • The Elsevier-SciHub story by Egon Willighagen Jun 24, 2017
        I blogged earlier today why I try to publish all my work gold Open Access. My ImpactStory profile shows I score 93% and note that with that 10% of the scientists in general score in that range. But then again, some publisher do make it hard for us...
      • As a PhD student, I was often confronted with Closed Access. by Egon Willighagen Jun 24, 2017
        It sounds like a problem not so common in western Europe, but it was when I was a fresh student (around 1994). The Radboud's University Library certainly did not have all journals and for one journal I had to go to a research department and s...
      • You are what you do, or how people got to see me as an engineer by Egon Willighagen Jun 11, 2017
        Source, Wikicommons, CC-BY-SA.Over the past 20 years I have had endless discussions into what the research is that I do. Many see my work as engineer, but I vigorously disagree. But some days it's just too easy to give up and explain things y...
      • New paper: "The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching" by Egon Willighagen Jun 10, 2017
        This paper was long overdue. But software papers are not easy to write, particularly not follow up papers. That actually seems a lot easier for databases. Moreover, we already publish too much. However, the scholarly community does not track softw...
      • May 29, Delft, The Netherlands: "Open Science: the National Plan and you" by Egon Willighagen May 19, 2017
        In less than ten days, a first national meeting is organized in Delft, The Netherlands, where researchers can meet researchers to talk about Open Science. Mind you, researcher is very broad: it is anyone doing research, at home (e.g. citizen scien...
      • GenX spill, national coverage, but where is the data by Egon Willighagen Apr 16, 2017
        First (I have never blogged much about risk and hazard), I am not an toxicological expert nor a regulator. I have deepest respect for both, as these studies are one of the most complex ones I am aware off. It makes rocket science look dull. Howeve...
      • The ACS Spring disclosures of 2017 #2: some history by Egon Willighagen Apr 14, 2017
        Bethany Halford adds some history about the sessions (see part #1):I believe Stu Borman was the first to cover the Division of Medicinal Chemistry’s First Time Disclosures symposium for C&EN, but it was Carmen Drahl who began the prac...
      • The ACS Spring disclosures of 2017 #1 by Egon Willighagen Apr 14, 2017
        At the American Chemical Society meetings drug companies disclose recent new drugs to the world. Normally, the chemical structures are already out in the open, often as part of patents. But because these patents commonly discuss many compounds, th...
      • Closed access book chapters, Bookmetrix, and job creations by Egon Willighagen Apr 1, 2017
        Enjoying my Saturday morning (you'll can actually track down that I write more blog posts then, than any other time of the week) with a coffee (no, not beer, Christoph). Wanted to complete my Scholia profile (gree work by Finn, arxiv:1703.042...

      Useful Chemistry
      • Matthew McBride wins Nov 2012 ONS Challenge Award by Jean-Claude Bradley Nov 16, 2012
        Matthew McBride, an undergraduate chemistry major at Drexel University working in the Bradley Laboratory, was awarded the November 2012 Open Notebook Science Challenge Award sponsored by the Royal Society of Chemistry.  ChemSpider founder Ant...
      • MiniSymposium Bradley Lab 2011 by Jean-Claude Bradley Oct 5, 2011
        I recently presented a 15 minute summary of the current research in my lab on September 29, 2011 at the Drexel University Department of Chemistry Faculty Mini-Symposium. The main project discussed was the Open Melting Point Collection done in coll...
      • Patrick Ndungu talk at Drexel on Nanotechnology by Jean-Claude Bradley Aug 18, 2011
        One of my former Ph. D. students, Patrick Ndungu (now at University of KwaZulu Natal, South Africa) will be speaking at Drexel University on Friday August 19, 2011 at 12:30 in Disque 109. Some Interesting Perspectives on the Integration of Nanoma...
      • Google Apps Scripts Workshop at Drexel University by Jean-Claude Bradley Aug 17, 2011
        Andrew Lang will be in Philadelphia next week and we will be running a workshop on Leveraging Google Spreadsheets with Scripts for Research and Teaching. Now that our institution is no longer providing Microsoft Office for students in the fall te...
      • Open Melting Point Collection Book Edition 1 by Jean-Claude Bradley Aug 11, 2011
        Several months of work through a collaboration between myself, Andrew Lang, Antony Williams and Evan Curtin have culminated in the publication of an Open Melting Point Collection Book. Like our other books on solubility and Reaction Attempts, the...
      • Rapid analysis of melting point trends and models using Google Apps Scripts by Jean-Claude Bradley Jul 19, 2011
        I recently reported on how Google Apps Scripts can be used to facilitate the recording and calculations associated with a chemistry laboratory notebook. (also see resource page)I will demonstrate here how these scripts can be used to rapidly disco...
      • Practical Tips on using Google Apps Scripts for Chemistry Applications by Jean-Claude Bradley Jul 14, 2011
        A few weeks ago I described our use of Google Apps Scripts, developed by Rich Apodaca and Andrew Lang, as an intuitive interface to information related to a chemistry laboratory notebook. Since then we have been using these tools to actively plan...
      • Open Notebook Science Talk at HUBbub 2011 by Jean-Claude Bradley Jul 1, 2011
        On April 6, 2011 I presented at the HUBzero Conference in Indianapolis on "Open Notebook Science: Does Transparency Work?".This presentation will first describe Open Notebook Science, the practice of making the laboratory notebook and all associat...
      • The 4-benzyltoluene melting point twist by Jean-Claude Bradley Jun 22, 2011
        Evan Curtin and I were in the lab this morning to follow up on our effort to curate the melting point of 4-benzyltoluene. I identified the next step to confirm an upper limit of -15 C:With the information available thus far from our experiments (...
      • Google Apps Scripts for an intuitive interface to organic chemistry Open Notebooks by Jean-Claude Bradley Jun 18, 2011
        Rich Apodaca recently demonstrated how Google Apps Scripts can be added to Google Spreadsheets to enable simple calling of web services for chemistry applications (gChem). Although we have been using web service calls from within a Google spreads...

      Noel O'Blog
      • Using WebLogo3 to create a sequence logo from Python by Noel O'Boyle May 5, 2017
        A sequence logo is a way to display the variation at particular positions of multiple-aligned sequences. Here I used WebLogo 3 to do this. The documentation is not great, even once you find it, and working out how to do my specific use case requir...
      • Whiskas statistics and the pitfalls of mean rank by Noel O'Boyle Jan 23, 2017
        In the fingerprint similarity paper I published last year, I made the following observation: "However the use of the mean rank is itself problematic as the pairwise similarity of two methods can be altered (and even inverted) by adding additional ...
      • Counting hydrogens in a SMILES string - The Rules by Noel O'Boyle Jan 14, 2017
        Hydrogens are not usually listed explicitly in a SMILES string, but instead can be inferred from a set of rules. To be precise, when reading a SMILES, the position of every hydrogen is known unambiguously once you know the rules. Oh - did I forget...
      • The clockwisdom of SMARTS by Noel O'Boyle Dec 30, 2016
        In earlier posts I discussed/investigated how stereochemistry is represented in SMILES. Here I'm going to try to figure out what I thought would be relatively simple, how to write a SMARTS pattern that matches a chiral molecule and all of its supe...
      • Open Babel 2.4.0 released by Noel O'Boyle Sep 23, 2016
        As announced by Geoff on the mailing list, Open Babel 2.4.0 is now available to download:I'm pleased to announce that Open Babel 2.4.0 has finally been released.This release represents a major update and should be a stable upgrade, strongly recomm...
      • My new thing - providing manuscript images as PDFs by Noel O'Boyle Aug 21, 2016
        My latest oeuvre (on the topic of which fingerprint is best) was published by J. Cheminf. a few weeks ago. For the first time, instead of providing the images as PNGs, I submitted them as PDFs.You see, John had worked me over. At the start, I thou...
      • Open Source Cheminformatics Toolkits - they keep on coming by Noel O'Boyle Aug 2, 2016
        It has been just over three years since I last surveyed the world of open source cheminformatics toolkits. So what's new?Kekule.js - This is a JavaScript toolkit by Chen Jiang with an associated publication in JCIM this year. JavaScript cheminform...
      • Your SD file will never be the same again...with ASCII depiction by Noel O'Boyle Jul 18, 2016
        A recent blog post showed how to depict a record in an SD file from within Vim. This of course is no help to those readers who have yet to successfully exit from a Vim session. But what if there was no need to create an ASCII depiction...because i...
      • Even more molecular depiction in Vim by Noel O'Boyle Jul 14, 2016
        Previous posts focused on popping up an ASCII depiction in Vim, but what doing something with the PNG output from Open Babel? Is there any way this can be viewed from Vim? Aged readers may remember a previous blog post of mine that looked into PNG...
      • The 7th Joint Sheffield Conference on Chemoinformatics - a real tweet by Noel O'Boyle Jul 13, 2016
        Just back from the Sheffield meeting, which takes place every 3rd year. Great meeting as ever - tribute was paid to John Holliday for the lion's share of the organisation. I got to meet some old friends and some new. For the first time at a meetin...

      petermr's blog
      • What is TextAndData/ContentMining? by pm286 Jul 11, 2017
        What is TextAndData/ContentMining? I prefer “ContentMining” to the formal legal phrase “Text and Data Mining” because it emphasizes all kinds of content - audio, photos, videos, diagrams, chemistry, etc. I chose it to asser...
      • Text and Data Mining: Overview by pm286 Jul 11, 2017
        Text and Data Mining: Overview Tomorrow The University of Cambridge Office of Scholarly Communication is running a 1-day Symposium on Text and Data Mining (https://docs.google.com/document/d/1l4N2fSFgpL3iMbjKC3IxHz7GpNVvERB5NzxqWp8jZQo/edit ). I h...
      • How Wikidata can change the world of scientific information 1/n by pm286 Nov 5, 2016
        We're getting involved in Wikidata! It will change the world of scientific (and other) information. So here is an emerging conversation, hopefully over several blog posts. Wicki: Hang on! What's Wikidata? And Wikimedia? I've heard of Wikipedia, bu...
      • The critical role of e-Theses: award acceptance speech at NDLTD by pm286 Jul 12, 2016
        I am honoured by this award; I ‘ll describe the current struggle for ownership of digital scholarly knowledge, emphasize young people and machine-understandable theses and suggest practices.   Early Career Researchers see the digital li...
      • "Dialogue" with Elsevier - story-2 ("Despicable" Legal Weasel Words) by pm286 May 26, 2016
        ContentMine is going to mine the whole scholarly literature (10,000 articles every day). We'd hoped to do this some months ago and one of the reasons is the massive pushback from major publishers. Technically, legally , politically. UK government ...
      • "Dialogue" with Elsevier - story-1 (Will Elsevier publish Crystallographic Data?) by pm286 May 24, 2016
        TL;DR. I continue to try to get public data out of Elsevier. I think I should be able to - every other publisher has no problem. After some not-very-useful replies Elsevier simply give up answering me. Over the last 7-8 … Continue reading &...
      • Taxi Ken and I discuss the UK's negotiations with Elsevier by pm286 May 23, 2016
        When I go the airport by taxi [1] I try to get the same taxi driver, Ken [2]. Ken is a shining example of why every citizen of the world needs access to the whole scholarly literature - open and … Continue reading →
      • Sci-Hub and my personal position on legality 5/n by pm286 May 6, 2016
        I have just blogged on the legal aspects of ContentMining: https://blogs.ch.cam.ac.uk/pmr/2016/05/06/sci-hub-and-legal-aspects-of-contentmining/ (which also contains links to previous blogs. These are general considerations but also relevant to th...
      • Sci-hub and Legal aspects of ContentMining 4/n by pm286 May 6, 2016
        Previous posts: https://blogs.ch.cam.ac.uk/pmr/2016/04/30/a-commentary-on-sci-hub-1-scholarly-publishing-is-broken/ https://blogs.ch.cam.ac.uk/pmr/2016/04/30/a-commentary-on-sci-hub-2n-why-it-matters-to-me-and-contentmine/ https://blogs.ch.cam.ac....
      • A commentary on Sci-Hub: 3/n Legal aspects by pm286 May 2, 2016
        Previous: https://blogs.ch.cam.ac.uk/pmr/2016/04/30/a-commentary-on-sci-hub-1-scholarly-publishing-is-broken/ https://blogs.ch.cam.ac.uk/pmr/2016/04/30/a-commentary-on-sci-hub-2n-why-it-matters-to-me-and-contentmine/ It’s impossible to discu...



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