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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




    So much to do, so little time
    • CSA Trust Grant – Call for Proposals by Rajarshi Guha Monday
      Applications Invited for CSA Trust Grant for 2017 The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research....
    • Endnote XML to HTML or LaTeX by Rajarshi Guha Dec 31, 2016
      Over the last few years I’ve been maintaining my publication list as a BibTeX file, managed by BibDesk. This is handy when writing papers, but it’s also useful to use this data to keep my CV updated or generate a publications...
    • Freedom from the IF: Impact Neutral Publishing by Rajarshi Guha Dec 26, 2016
      I came across a post from Jan Jensen a few months ago about a GRC meeting that he had attended. What caught my eye however, was his comment on “impact neutral” publishing. Specifically, he mentions For me “impact neutrality&rdquo...
    • Deep Learning in Chemistry by Rajarshi Guha Nov 8, 2016
      Deep learning (DL) is all the rage these days and this approach to predictive modeling is being applied to a wide variety of problems, including many in computational drug discovery. As a dilettante in the area of deep learning, I’ve been fo...
    • A Report from a Stranger in a Strange Land by Rajarshi Guha Oct 26, 2016
      I just got back from ACoP7, the yearly meeting of the International Society of Pharmacometrics (ISoP). Now, I don’t do any PK/PD modeling (hence the “strange land”) but was invited to talk about our high throughput screening plat...
    • From Algorithmic Fairness to QSAR Models by Rajarshi Guha Aug 8, 2016
      The topic of algorithmic fairness has started recieving a lot of attention due to the ability of predictive models to make decisions that might discriminate against certain classes of people. The reasons for this include biased training data, corr...
    • Database Licensing & Sustainability by Rajarshi Guha May 14, 2016
      Update (07/28/16): DrugBank/OMx have updated the licensing conditions for DrugBank data in response to concerns raised earlier by various people and groups. See here for a detailed response from Craig Knox A few days back I came across, via my Twi...
    • SLAS 2017: Let There Be Light: Informatics Approaches to Exploring the Dark Genome by Rajarshi Guha May 11, 2016
      I’m organizing a symposium at the 2017 SLAS meeting in Washington D.C in the Data Analysis and Informatics track. The topic of the symposium focuses on informatics approaches that shed light and explore the dark genome. The description is gi...
    • Differential Dose Response – Some More Exploration by Rajarshi Guha May 7, 2016
      This is a follow on to my previous post that described a recent paper where we explored a few ways to characterize the differential activity of small molecules in dose response screens. In this post I wanted to highlight some aspects of this type ...
    • Analysing Differential Activity in Dose Response Screens by Rajarshi Guha May 1, 2016
      My colleagues and I recently published a paper where we explored a few methods to identify differential behavior in dose response screens. While there is an extensive literature about analyzing differential effects in genomic data (e.g. mciroarray...

    chem-bla-ics
    • Talk: "Making open science a reality, from a researcher perspective" by Egon Willighagen Sunday
      Slide from the presentations witha screenshot of theWoordenboek Organische Chemie.Last week I was in Paris (wonderful, but like London, a city that makes you understand Ankh-morpork) for the AgreenSkills+ annual meeting. AgreenSkills+ is a program...
    • Open Science is already a thing in The Netherlands by Egon Willighagen Feb 18, 2017
      It has been hard to miss it: the Dutch National Plan Open Science (doi:10.4233/uuid:9e9fa82e-06c1-4d0d-9e20-5620259a6c65). It sets out an important step forward: it goes beyond Open Access publishing, which has become a tainted topic. After all, g...
    • Wikidata-powered citation lists with citation.js by Egon Willighagen Jan 3, 2017
      I don't get enough time with the kids as I would like, but if your son is doing interesting coding projects it makes that a lot easier. One project he is working on is citation.js, a JavaScript library to edit bibliographies. It has become really ...
    • "10 everyday things on the web the EU Commission wants to make illegal" #04 by Egon Willighagen Jan 3, 2017
      Fourth example is harder then the third and I hope I got the translation of Julia Reda's example in good way. The starting point is simple enough, bookmarking things where an image is used. However, I am less sure to what extend we use this i...
    • EPA CompTox Dashboard IDs in Wikidata by Egon Willighagen Jan 2, 2017
      After Antony Williams left the ChemSpider team, he moved on to the EPA. Since then, he has set up the EPA CompTox Dashboard (see also doi:10.1007/s00216-016-0139-z [€]). And in August he was kind enough to upload mappings between InChIKe...
    • "10 everyday things on the web the EU Commission wants to make illegal" #03 by Egon Willighagen Dec 30, 2016
      The third example in this series is not too hard to explain.03. Posting a blog post to social mediaBecause many of you are familiar with blogging and many of you blog yourself, you know what this one is about. The way I understood it, it will be l...
    • "10 everyday things on the web the EU Commission wants to make illegal" #01 by Egon Willighagen Dec 30, 2016
      OK, after moving to the second example, I realized the subtle difference with the first: I got example 01 and 02 mixed up, and while the previous post was really discussing Julia's second example. Example 01 is really about snippets of publication...
    • "10 everyday things on the web the EU Commission wants to make illegal" #02 by Egon Willighagen Dec 28, 2016
      OK, let me first say that I hope Julia Reda does not consider herself a publisher. If you did not get the above joke, then continue reading.This post is an attempt to translate the proposed copyright laws to, well, research. The choice of words is...
    • Facts, Data and Open Data by Egon Willighagen Dec 23, 2016
      Source, CCZero.I was recently asked my experiences around data sharing, and in particularly the legal aspects of it. Because whether we like it or not (I think "we" generally do not like it and I see many scholars ignore it), society has an impact...
    • The SWAT4LS poster about eNanoMapper by Egon Willighagen Dec 18, 2016
      SWAT4LS was once again a great meeting. I doubt I will find time soon enough to write up notes, but at least I can post the eNanoMapper poster I presented, which is available from F1000Research:Willighagen E, Rautenberg M, Gebele D et al. Answerin...

    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
    • 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...
    • 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...

    petermr's blog
    • 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...
    • 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...



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