JNI InChI 0.4.1 released

March 30, 2007

From Sam Adams:
I’ve just released a new version of JNI InChI – 0.4.1. There’s a jar up on sourceforge, and a tag on the svn (http://jni-inchi.svn.sf.net/svnroot/jni-inchi/tags/jniInChI-0.4.1/). The main change is that the code is now safe for use in multi-threaded environments. The native code havsn’t been changed at all, only the java code, so existing binaries will continue to work.

Maven2 users can obtain it from the WWMM maven repo at http://wwmm.ch.cam.ac.uk/maven2/ using groupId net.sf and artifactId jniinchi.

JNI InChI is a better way of calling the InChI libraries from Java applications than using System.exec or the Java 1.5 equivalents.

SPECTRaT is go!

March 16, 2007

The application for funding for SPECTRa-T (Theses) from JISC has been successful. SPECTRaT will kick off at the start of April, and will be looking at extracting data from chemistry theses and depositing both in digital repositories, and will be collaborating with researchers on the SciBorg project for natural language processing.

Congratulations to all the SPECTRa team!

This was almost inevitable, with the benefit of hindsight. It seems that the phrase “Open Data” is now being used in the context of transparency / translucency of attention data.

Do we stick to our guns or find a more specific phrase to use?

This presentation (via) contains some interesting material, especially for Open Data from the section of the summary document entitled “Access to scientific data from publicly funded sources”. Cherry picking: –

… in deciding how or where to publish their most recent work, respondents cited the
dissemination of research results (e.g., through a journal with a high degree of circulation and
relevant readership) as the leading criterion; “prestige”—meaning their work would be placed on a
list of select, highly-relevant journals of which publication in any of them could lead to academic
promotion or greater prospects for research funding—ranked second …

This surprised me, although the actual behaviour may not be accurately reflected by the responses.

The majority of survey respondents … had
used or tried to use data (that they personally did not produce) from publicly funded sources …

Of those respondents … almost one-quarter (24 percent) experienced difficulties in obtaining such data.

… the two most highly-cited problems [in obtaining data from publicly funded research] were a substantial delay in the transfer of data, and that
access to data was denied…

Of those respondents who reported experiencing difficulties in obtaining data from publicly
funded sources, most (70 percent) reported that such difficulties had “some negative effect(s)”
upon their research; 10 percent experienced “serious negative effect(s).”

Twenty-nine percent of those respondents who had been denied access to data from a publicly funded source reported that they were not provided a reason for being denied access; 16 percent
reported that they were denied access to data from which results already had been published.

Note that this doesn’t cover data from publicly funded sources which isn’t made available at all, and so represents the tip of the iceberg.

Tickled by the news that BioMed Central is selling merchandise with various OA journal logos on. Before the imagination runs amok with the idea that this a potential business model for OA publishing (Stevan Harnad figurines? Peter Suber mobile phone facias?), note that BMC are giving away their commission to charity.

The Chem Central T looks quite smart but I’m not sure about the one with the slogan “biology direct” pointing at the armpit.

More on Erlang

March 9, 2007

Toby White put me on to this blog entry about Erlang whence I found this Eclipse plugin for Erlang. I’m glad I’m not the only one who found the expression termination characters confusing, it reminded me of my early days learning pascal. Anyway, interesting stuff – I wonder if Erlang has will and ability to become more mainstream?

SPECTRa in the news

March 8, 2007

Novel search engine matches molecules in a flash” is an article referencing an RSC proceedings paper (DOI: 10.1098/rspa.2007.1823) describing a novel method of similarity searching. Interesting stuff, and SPECTRa is mentioned near the end by Prof. Rzepa.