JCBblognotes

=UsefulChem Blog Notes=


 * Started: September 20, 2006**
 * Ended: In Progress

[|Friday, July 29, 2005]**
 * Establishes purpose of the blog
 * //What we are trying to do here is identify specific problems and objectives in chemistry, as stated by researchers in their articles.//
 * Establishes methodology
 * List of search terms for Google Scholar or Scirus


 * [|Tuesday, November 1, 2005]**
 * Documents [|Find-A-Drug] Contact


 * [|Thursday, November 17, 2005]**
 * This post is not written by Jean-Claude or one of his students. This post is presented by science writer David Bradley. As such, it demonstrates th "collaborative nature" of blogging.
 * This is the first time "[|Chemists without Borders]" (collaboration site) is mentioned.

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 * [|Thursday, November 17, 2005]**
 * This is the first post to mention enoyl reductase and malaria
 * Sites Find-A-Drug


 * [|Saturday, November 19, 2005]**
 * Mentions the use of [|Chmoogle (now e-molecules)]; this is a "search engine for chemicals"
 * In a later post ([|Sunday, November 27, 2005]), Jean-Claude says, "So it seems Chmoogle should be used cautiously to determine commercial availability."


 * [|Monday, November 28, 2005]**
 * This post discusses the creation of a new blog to house chemical compunds; "The aim of this blog is to keep track of information on the compounds we wish to synthesize and the reagents necessary to do so."
 * "I want to see if others can understand what I am saying and add the rest of the info. The most useful info is of course the commercial availability and the cost."
 * "Yes, we are using a blog as a database. That is certainly not the most efficient way to store and retrieve information but with relatively few compounds I think the advantages are significant. The blog is accessible by anyone and is archived quickly by search engines, especially Blogsearch. This is a free and hosted solution so anyone can replicate this model immediately in other fields. The blog provides an intuitive environment for both humans and autonomous agents. Since Word now has a plug-in to update Blogger, we might consider VBA as a quick hack to carry out some of the automation."
 * "And perhaps most importantly, a blog represents an easy to way to create an RSS-CML (Chemical Markup Language) feed so autonomous agents can read the feed as chemical information. See Rzepa and Murray-Rust references here for more info on CML. ChemSketch can export CML but I have been able to have that output interpreted correctly by the RSS-CML reader mentioned in those references. This would be a useful thing for the programmers to figure out."


 * [|Tuesday, November 29, 2005]**
 * In this post, we see the benefits of collaboration; "I think we have made some good progress in moving towards automation today, thanks to people like Ruslan who figured out how to use ChemBasic to spit out [|molecule names]form the list of anitmalarials posted [|in this blog previously]."
 * "If this seems confusing to people who just fall onto this post, keep in mind that our objective is to synthesize the most promising anti-malarial candidates and have them tested ASAP for in vitro on red blood cell infection assay."


 * [|Wednesday, November 30, 2005]**
 * This mentions an [|interview with Peter Murray-Rust]


 * [|Sunday, December 4, 2005]**
 * This discusses the release of OpenBabel 2.0; "It is an extremely comprehensive chemical data conversion tool that has both command line and a GUI interface. And it is all free open source."
 * Jean-Claude also uses the forum to ask for help with CMLRSS demonstrating the "collaborative" nature of blogging.


 * [|Thursday, December 8, 2005]**
 * This is the date that Jean-Claude launched his UsefulChem Wiki.


 * "I have created a Wiki to keep a concise and updated summary of the major project that we are pursuing in the UsefulChem blog. As we are getting more volunteers it will easier for them to get the bigger picture and understand how they can contribute immediately."


 * [|Sunday, December 18, 2005]**
 * This posts discusses the e-malaria project at Southampton University. It deomonstrates that there are others (globally) working toward the dame goal.


 * [|Wednesday, December 21, 2005]**
 * This post discusses the Synaptic Leap; "[|The Synaptic Leap] is another initiative to coordinate open source biomedical research...It will be very interesting to see how all of these efforts co-evolve and leverage each other."


 * [|Saturday, December 31, 2005]**
 * This post compare Chmoogle to QueryChem for single searches ("With all of these advantages, QueryChem is now my first choice for **single search** open content chemical information. For [|**ongoing monitoring**] of our [|UsefulChem] project I am still going to use CAS number searches in MSN ([|exportable via OPML]) because QueryChem does not yet provide RSS feeds for searches.).


 * What is interesting is that Jean-Claude's interests are consistent with his posts; he wants to be able to access the most information via the least expensive but most efficient method. Two reasons he cites are


 * **"This is the big one:** the results in QueryChem take you directly to the pages of the commercial suppliers. In a Chmoogle search, the results only take you to the general company URL, where you have to do the search over again."
 * :A QueryChem search does a lot of work for you. It figures out the possible names for a compound then throws that back into Google or Google Scholar and then shows where those names appear in the results. That saves a lot of manual labor."


 * [|Monday, January 16, 2006]**
 * This is an interesting post because it discusses the complications of the various out-put formats.
 * "Ruslan has been working on this type of processing but unfortunately [|it is in Perl], which is inconvenient for our current team members, who have little programming experience. What would be nice is the translation of this type of code to VBA for Excel...Hopefully we'll come across somebody with VBA experience willing to help."


 * [|Tuesday, February 7, 2006]**
 * This most mentions the experiments blog:
 * "I have set up a [|separate blog] to put all experimental details for the UsefulChem project, at least for experiments done in my lab. The plan is to use about 300 posts per Blogger blog as one laboratory notebook. Each post is one experiment and open for comment."


 * [|Tuesday, March 7, 2006]**
 * This post explans CMLRSS:
 * "Having a working CMLRSS reader is an important step in cheminformatics because it will enable the user to manipulate molecules as molecules, not just static images. For example the subscriber would be able to rotate the molecule, view it using different representation formats, measure bond lengths, etc. directly inside of the reader."
 * "[|CML] (Chemical Markup Language) is a kind of XML that allows for the representation of chemical information."


 * [|Monday, March 20, 2006]**
 * This discusses an interview with Steve Braynt of PubChem.


 * [|Tuesday, May 16, 2006]**
 * This post talks about other places where chemists share information about chemistry (that isn't usually published):
 * "Thanks to [|Sciencebase], I have found a [|new forum] dedicated to discussing and posting chemical experiments and results that don't make it to standard publications."


 * [|Thursday, July 13, 2006]**
 * This post deals with the patent process:
 * "he purpose of a patent is to prevent people from doing things without permission (generally for a fee) from the patent holder. That's what gives patents monetary and strategic value. It may be possible to get a special license from the patent holder for humanitarian applications but that sounds like an added layer of complexity and cost that is not present in open source public domain solutions."
 * "The other issue, in my experience as a chemist, is that chemical patents are often written in a way that makes it difficult to reproduce some of the experiments. There are generally some detailed examples but much of the content tends to be written to be as broad as possible, covering reactions and conditions that have not been done. I've been through the patent writing process with attorneys a few times and it is a very different mindset compared to writing an article with the aim of truly sharing knowledge."
 * "Concerning the issue of this being a Chinese patent application and thus not applicable to the rest of the world, that is a dangerous assumption. The only way to know is to search for similar filings in other countries. I would think that there is a good chance that there is a US filing if there is a Chinese one. But different countries have different timelines for disclosing patent filings. Basically it would require some legwork to really know."


 * [|Friday, July 21, 2006]**
 * This mentions an article about the UsefulChem project in C&E News. This is an important milestone because it means that the C7E community is now taking open source chemistry seriously enough to discuss it in a mjaor discipline-specific publication.


 * [|Tuesday, August 8, 2006]**
 * This post mentions another open source blog; this demonstrates the collaborative nature of UsefulChem.


 * [|Monday, August 21, 2006]**
 * This post is about the publishing opportunities through Synthetic Pages. Again, this is just a documentation of the collaborative nature of the work.


 * [|Sunday, August 27, 2006]**
 * This post links over to an extremely useful presentation delivered by Ginger Taylor of The Synaptic Leap (collaboration site)


 * [|Tuesday, August 29, 2006]**
 * This is a useful post explaining how UsefulChem works:
 * We can check the hourly progress of an experiment by clicking on the rencet changes tab in the wiki; this gives an hourly update of the work
 * I wonder if Jean-Claude checks the lab work from his office to see if his students need help? For example, was he able to comment on the work when he was cross country at the ACS conference? Sure see my comments on the [|wiki history] during Sept 10-14, 2006.


 * It makes the argument that this "open lab notebook" approach is better suited for a wiki than a blog because the third party time stamp is available:
 * "That way it is possible to find out not only what happened but also HOW the student, supervisor and colleagues arrived at the results, presented arguments in the discussion and came to their conclusions. "
 * Wikis, however, don't have the same potential for RSS feed, and that is a down side to using them.
 * The post recapiltulates the spirit of the collaborative nature of the project:
 * "We appreciate the feedback we have been getting so far and we welcome future comments on any aspect of our work from chemists anywhere."


 * [|Saturday, September 2, 2006]**
 * This post discusses two other leaders in the "open" movement: Peter Murray-Rust and Egon Willighagen.


 * [|Saturday, September 9, 2006]**
 * This post reminds participants to code information correctly so that the readers can pick up and document work; this is an example of "practice."


 * [|Tuesday, Spetember 12, 2006]**
 * This is a summary post of the ACS meeting Jean-Claude attended. What is most striking is the number of talks/presentations about various methods to share information.


 * [|Sunday, September 17, 2006]**
 * This post provides a link to Jean-Claude's talk at the ACS meeting. The talk is an excellent summary of the UsefulChem project.


 * [|Wednesday, September 27, 2006]**
 * This post discusses the recent conversation on the BO mailing list about definitions. It links to another of Jean-Claude's blogs where he explores the use of a new term, Open Notebook Science, to clarify misunderstandings between what his lab does and Open Source Code in computing.
 * What is most striking is that this post, and its extensions, demonstrate the usefulness of this conversation in this community.


 * [|October 31, 2006]**
 * This is a nice post that outlines an open notebook approach to procedure. I think this is useful for my students, but also demosntrates the collaborative nature of blogging; "am also hoping that publishing our experimental intentions can save us from making unnecessary mistakes by obtaining feedback from others before we start executing."