Check out the new site at learncheminformatics.com!
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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
      • Alzheimer’s disease, PaDEL-Descriptor, CDK versions, and QSAR models by Egon Willighagen Aug 15, 2016
        A new paper in PeerJ (doi:10.7717/peerj.2322) caught my eye for two reasons. First, it's nice to see a paper using the CDK in PeerJ, one of the journals of an innovative, gold Open Access publishing group. Second, that's what I call a graphical ab...
      • The Groovy Cheminformatics scripts are now online by Egon Willighagen Aug 13, 2016
        My Groovy Cheminformatics with the Chemistry Development Kit book sold more than 100 times via Lulu.com now. An older release can be downloaded as CC-BY from Figshare and was "bought" 39 times. That does not really make a living, but doe...
      • Use of the BridgeDb metabolite ID mapping database in PathVisio by Egon Willighagen Jul 17, 2016
        A long time ago Martijn van Iersel wrote a PathVisio plugin that visualizes 2D chemical structures of metabolites in pathways as found on WikiPathways. Some time ago I tried to update it to a more recent CDK version, but did not have eno...
      • Setting up a local SPARQL endpoint by Egon Willighagen Jul 10, 2016
        ... has never been easier, and I have to say, with Virtuoso it already was easy.Step 1: download the jar and fire up the serverOK, you do need Java installed, and for many this is still the case, despite Oracle doing their very best to totally rui...
      • Metabolomics 2016 Write up #1: some interesting bits by Egon Willighagen Jul 8, 2016
        A good conference needs some time to digest. A previous supervisor advised me that a conference travel of 5 days takes 5 full day to follow up on everything. I think he is right, though few of us actually block our schedules to make time for that....
      • Harmonized identifiers in the WikiPathways RDF by Egon Willighagen Jul 2, 2016
        Biological knowledge should not only be capturedin nice graphics, but should be machine readable.Public domain image from Wikipedia.WikiPathways described biological processes. Entities in these processes are genes, gene products, like miRNAs, pro...
      • Two Apache Jena SPARQL query performance observations by Egon Willighagen Jul 2, 2016
        Doing searches in RDF stores is commonly done with SPARQL queries. I have been using this with the semantic web translation of WikiPathways by Andra to find common content issues, though sometimes combined with some additional Java code. For ...
      • New Paper: "Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources" by Egon Willighagen Jun 25, 2016
        Andra Waagmeester published a paper on his work on a semantic web version of the WikiPathways (doi:10.1371/journal.pcbi.1004989). The paper outlines the design decisions, shows the SPARQL endpoint, and several examples SPARQL queries. These includ...
      • Wikidata showing chemical properties with references by Egon Willighagen Jun 5, 2016
        As you have seen in my blog, I'm a fan of Wikidata. Because of the Open nature, it's creating an enormous eco-system, in which many scientists are involved and with innovative visualizations. Data comes from many trusted databases, but the complex...
      • Comparing sets of identifiers: the Bioclipse implementation by Egon Willighagen May 18, 2016
        Source: WikipediaThe problemThat sounds easy: take two collection of identifiers, put them in sets, determine the intersection, done. Sadly, each collection uses identifiers from different databases. Worse, within one set identifiers from multiple...

      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
      • My new thing - providing manuscript images as PDFs by Noel O'Boyle Sunday
        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...
      • Basic Graphviz input file generator in Python by Noel O'Boyle Jul 12, 2016
        Generating a Graphviz Dot input file is fairly simple, so I tend to code it up myself rather than use an existing library. However the need to normalise the node names complicates things a little bit. Here's a copy of the one I wrote today. Note t...
      • Syntax highlighting for SMILES files in Vim by Noel O'Boyle Jul 8, 2016
        An image in a recent blogpost showed how the default syntax highlighting (*) in Vim looks when applied to SMILES files. A splash of pink here and there to brighten things up on a dull molecule. It's definitely doing something, but what it's doing ...
      • More molecular depiction in Vim by Noel O'Boyle Jun 16, 2016
        The reception for my previous blog post on ASCII depiction in Vim was somewhat muted even, dare I say, lukewarm. Buoyed by this response, I updated that script to handle quoted SMILES strings (as found in my Python scripts, for example). And here ...
      • SMILES depiction in Vim by Noel O'Boyle Jun 13, 2016
        I spend a lot of time scrolling through files of SMILES in Vim, and copying and pasting SMILES into viewers. This is now a thing of the past. I bring you (from the depths of time) molecule depiction within Vim.Using the script below (paste it into...
      • Open Babel presentation at MIOSS 2016 by Noel O'Boyle May 21, 2016
        Thanks again to George Papadatos, Mark Forster, et al for the invitation to present at the 2016 reboot of MIOSS (Molecular Informatics in Open Source Software). You may remember the earlier one back in 2011.I gave a presentation on the Open Babel ...

      petermr's blog
      • 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...
      • A commentary on Sci-hub: 2/n. Why it matters to me and ContentMine by pm286 Apr 30, 2016
        In my previous post , catalyzed by Sci-Hub, https://blogs.ch.cam.ac.uk/pmr/2016/04/30/a-commentary-on-sci-hub-1-scholarly-publishing-is-broken/ I argued that scholarly publishing is completely broken. It’s now lost a huge amount of respect, ...
      • A commentary on Sci-hub: 1. Scholarly publishing is broken by pm286 Apr 30, 2016
        Many of you will already have read of Science Magazine’s account of Sci-Hub, the “pirate” site for scholarly publications. “Science” is often seen as one to the “top three” outlets, along with Nature and C...
      • Tummy bug 2: The scientific literature teaches us about Isospora by pm286 Apr 29, 2016
        In the previous post we showed how ContentMine could give immediate knowledge about a scientific topic - we analysed “Isospora”, which is a nasty tummy bug. Let’s just read Wikipedia to get some idea of the language we’ll n...



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