Chemistry Central Blog
It's certainly informative and engaging, and shows some real chemistry in action.
Posted by Jan Kuras at 11:14 Comments (0)
Jan Kuras joins Chemistry Central
Greetings! I join Chemistry Central as the new Associate Publisher.
After a brief sojourn away from science publishing - and a couple of exciting vacations - I am back on familiar territory.
I garnered an interest in how chemists can efficiently communicate their research findings when I was studying chemistry, and then specializing in analytical chemistry. My first meaningful employment was at Thomson Scientific (in what was then Derwent). I worked on pharmaceutical information products, and was involved in the development of the company’s first structure searchable and web-based databases.
This stimulated an interest in the application of Web technologies to search and display scientific data. I joined BioMedNet and then ChemWeb at Elsevier. My roles encompassed product development, publisher relations and community site development, and I was fortunate to collaborate with some prestigious publishers and database vendors. We were motivated by producing intuitive website functionality and easily accessible information. Our highest usage was always for free access, high quality journals and databases.
I am now pleased to be joining Chemistry Central, where we are striving to accelerate the growth in open access publishing of chemistry research, and I look forward to keeping you informed through the Chemistry Central blog.
Posted by Jan Kuras at 14:07 Comments (0)
Chemistry Central Journal author joins the editorial board
We are delighted to announce the appointment of Dr Sébastien Sauvé, associate professor in the department of chemistry at the university of Montreal, Canada, to the editorial board. He will act as an editorial adviser on analytical, aquatic and environmental chemistry, in addition to geochemistry and mass spectrometry.
Dr Sauvé's numerous areas of research interest include: soil and environmental chemical and ecotoxicological evaluations, such as the environmental fate of contaminants and pharmaceuticals; quantification of the occurrence and transformation of nanoparticles and nanotechnology in the environment; and chemical speciation, including the kinetics of complication and dissociation, as well as adsorption and desorption rates at the solid-liquid interface. His research also focuses on creating conceptual and computational models that integrate environmental fate, chemical speciation and bioavailability.
Dr Sauvé recently published a preliminary communication in Chemistry Central Journal reporting the use of graphite
furnace atomic absorption spectrometry in studying the effects of two complexing agents on the fractionation
of beryllium in human serum.
Preliminary communication
Study
on the effects of nitrilotriproprionic acid and
4,5-dihydroxy-1,3-benzene disulphonate on the fractionation of
beryllium in human serum using graphite furnace atomic absorption
spectrometry
Chadi H Stephan, Michel Fournier, Pauline Brousseau, Sebastien Sauve
Chemistry Central Journal 2008, 2:10 (14 May 2008)
[Abstract] [Provisional PDF]
Posted by Gino D'Oca at 10:15 Comments (0)
Chempedia: "a free and continuously-updated" chemical compound encyclopaedia
Each compound monograph outlines information about the "structure, uses, history, and significance of a chemical compound". Users can search for compounds through the 'ChemWriter Structure Editor' or by text using a title, CAS Number, or PubChem CID. There is also the option to search the compound listings alphabetically or by most recent items.
The compound entries can be updated as soon as possible to reflect newly available information. Here users are well placed to know when an existing Wikipedia compound monograph ought to appear in Chempedia yet does not, when an existing monograph needs to be updated, or when a new monograph has been written and needs to be linked. All users need to do in order to create a new or updated link from Chempedia to Wikipedia, is to provide the Wikipedia link via the 'create' tab found on the site's main menu.
Posted by Gino D'Oca at 16:18 Comments (0)
New, free-to-access life sciences search engine
A new, free-to-access life sciences search engine has been recently made available to the general public. NextBio allows users to search over 10,000 public experimental results, 1.2 billion data points, and 16 million PubMed literature abstracts, making "massive amounts of disparate biological, clinical and chemical data from public and proprietary sources searchable, regardless of data type and origin....".
The search engine's framework, which connects heterogeneous data and textual information, was previously only provided in an "enterprise version" for life science R&D and drug development, with notable users including Johnson & Johnson Pharmaceutical Research & Development. The "enterprise accounts" differ from the free version in that they include "added data integration services, security and support".
The research areas covered by NextBio's publicly searchable data range from pharmacogenomics to oncology. Functionality exists to allow users to import their own analysed experimental results, where they can choose to share their data with the network or restrict access to a limited audience. Users can also create their own profiles to more easily develop collaborations with other scientists.
NextBio's founders state that it
"...provides a unique opportunity for the research
community to collaborate through information sharing and to perform an important
part of their biological work in silico... [allowing users]... to glean new
insights into gene function, disease progression and compound effects, as well
as into their own studies using the world's quality public experiments..."
There
are plans to incorporate further content into the platform in due course, such as
sequence-centric and phenotypic data types. Helpful and informative video demonstrations can be found on the site, offering an overview of the initiative's "open biology" ethos, as well as a tutorial on how to use the search engine.
Posted by Gino D'Oca at 16:19 Comments (0)
Open database for insect semiochemicals
To continue our theme of providing overviews of free-to-access chemical databases, I feel Pherobase, a interesting database of insect behaviour modifying chemicals, to be well worth a mention.
The database, hosted by the chemical ecology group, HortResearch, New Zealand, is aimed at "convert[ing] scientific data and knowledge from the literature and publish[ing] peer-reviewed information about behavioural modifying chemicals in insects into electronically searchable database entries." Chemical signals are the main channel of communication in arthropods, especially insects, finding uses in, amongst other things, sexual attraction and defence. The project's author believes the database will "...definitely aid and [accelerate] the process of semiochemicals' (Ed: chemical substance that carries a message) identification and... will provide an overview of the hetero-specific overlap in the chemical signals between different animal groups."
The database, which has now grown to over 50,000 entries - of which 3,000 contain details on molecules -, also contains mass spectral data on over 1,500 of the compounds. Users can search by text, or browse a large number of categories, including genus, species, and functional group, but also application, such as 'lure and kill' and 'mating disruption'. In addition to having an interactive Jmol molecular model, each compound page contains links to spectra, as well as references regarding synthesis and behavioural function.
Pherobase is yet another
example of a free-to-access database, which benefits from being enriched and augmented by contributions from
interested specialists, and that in spite of attracting a somewhat
niche audience, nonetheless has high practical utility.
***
On a related note, it is
worth highlighting Anthony Williams' (ChemSpider) review of the
status of public chemical databases that was recently published in BioMed
Central's Current Opinion in Drug Discovery and
Development. The following is an excerpt from the abstract:
“...The increasing array of chemistry-related resources that are now available provides chemists with a direct path to the information that was previously accessed via library services and was limited by commercial and costly resources. The diversity of the information that can be accessed online is expanding at a dramatic rate, and the support for publicly available resources offers significant opportunities in terms of the benefits to science and society. While the data online do not generally meet the quality standards of manually curated sources, there are efforts underway to gather scientists together and 'crowdsource' an improvement in the quality of the available data...” Public chemical compound databases: Current Opinion in Drug Discovery and Development 2008, 11:393-404 (18 April 2008).
Posted by Gino D'Oca at 16:14 Comments (0)
Chemistry Central appoints new Section Editor
We are delighted to announce the appointment of Professor Yang Gan (Harbin Institute of
Technology, China) as Section Editor for geochemistry, nuclear and radiochemistry and
surface/interfacial chemistry.
Prof Gan, who also serves as an editorial adviser for physical chemistry, joined the board in October 2007. His research interests lie in the use of Atomic Force Microscopy (AFM) in various areas, such as in the study of the interaction of oxide particles in high salt concentrations, the relationship between atomic scale structure and surface charge behaviour of hydroxylated alpha alumina, and crack extension behaviour in brittle solids.
Posted by Gino D'Oca at 12:02 Comments (0)
Chemistry Central to attend the 235th ACS national meeting in New Orleans
Chemistry Central will be exhibiting and speaking at The 235th American Chemical Society National Meeting, in New Orleans from 6-10th of April.
Do visit us at booth 1305 in the Morial Convention Center and hear us speak on 'Open access: Toward the mainstream?' at 11.35 a.m. on Monday the 7th of April (Division: Division of Chemical Education; Session: Using Social Networking Tools to Teach Chemistry).
Posted by Gino D'Oca at 16:08 Comments (0)
CAS agrees to cooperate with Wikipedia
In a positive turnaround Chemical Abstracts Service (CAS) has announced that it will support the 'CAS Number Validation project' started at Wikipedia Chemistry to assist in producing a curated dataset.
"CAS, a division of the American Chemical Society... will contribute to the Wikipedia project... to help provide accurate CAS Registry Numbers for current substances listed in Wikiprojects-Chemicals... that are of widespread general public interest...". The statement goes on to say that "CAS views Wikipedia as an important societal tool for the general public, and this collaboration with Wikipedia is in line with CAS' mission as a Division of the American Chemical Society."
The declaration comes after CAS had earlier made clear its objection "to anyone encouraging the use of SciFinder and STN to curate third-party databases or chemical substance collections, including the one found in Wikipedia. SciFinder and STN are provided to researchers under formal license agreements, under which the researchers agree to refrain from using these tools to build databases. We urge and expect those researchers to respect the explicit terms of the agreements they have entered into..."
CAS's agreement to
cooperate comes on the back of discussions with Martin Walker of WP:Chem and the ChemSpider
Advisory Group, in addition to much debate that ensued elsewhere.
The aim of the validation project is to address various concerns, which
include CAS numbers not matching the structure drawn in the Wikipedia's 'Chemical
Box' or 'Drug Box'. The import of CAS's cooperation was reiterated on the ChemSpider blog: "...there is general agreement by all participants at WP:Chem
that CAS Numbers have value... so the presence of a CAS number in the
[Wikipedia] boxes makes absolute sense and, of course, the correct CAS number
for the structure makes sense in an encyclopedia."
Posted by Gino D'Oca at 11:18 Comments (0)
Open source organic dictionary created
An open source dictionary of organic chemistry has recently been compiled for word processors.
The dictionary, hosted by ChemSpy, was put together by Adam Azman - student in the chemistry department at the University of North Carolina at Chapel Hill - who decided to create his own because of the lack availability of free chemical dictionaries.
The dictionary, which can be downloaded on the ChemSpy site, is in a standard “.dic” format, and so can be opened in NotePad to view - and if desired, edit - the entire content. Instructions for installing it on Microsoft Word OpenOffice can be found in the download together with licensing information - the dictionary is covered by a Creative Commons Attribution License.
As Azman concedes, further improvements will be needed to the 18,000-word resource, such as in eliminating some misspellings and including UK spellings. To help expand the dictionary's content, ChemSpider has also provided 'many hundreds of thousands of chemical names and terms' that can be harvested from. The project highlights yet another interesting open source avenue that scientists are pursuing.
Posted by Gino D'Oca at 16:21 Comments (1)
Open database for structural biologists
Proteopedia, a new open database for biologists and chemists, has been recently launched. The project's scope is the "[collection and dissemination of] structural biological and biological knowledge about proteins, RNA, DNA, and their assemblies and interacting small molecules in a manner that is... accessible...".
At present the database - which was created in 2007 by Joel Sussman, Eran Hodis and Jaime Prilusky, researchers at The Weizmann Institute of Science, Israel - has around 50,000 searchable entries, including one page for each entry in the Protein Data Bank (PDB). Most of the pages are titled with a four-character PDB identification code, and the database is updated regularly to assimilate new data released by the PDB. In addition to those identified with a PDB code, there are also entries dedicated to particular molecules and topics, such as Glycine, Antibodies and Serine Protease.
The database is another example of numerous new projects whose aim is to provide open data whilst also embracing new technologies for their display. The project's broader three-fold aims are thus:
- To serve as a forum for scientists to share, retrieve and discuss information related to proteins, macromolecules, and small molecules and chemicals of interest.
- To continue to develop the concept of tying text to three-dimensional, interactive images.
- To maintain low barriers for contribution.
Posted by Gino D'Oca at 11:53 Comments (0)
Chemistry Central to attend the 2008 Fruehjahrssymposium in Rostock
The 10th Frühjahrssymposium (young scientists conference on chemistry) takes place in Rostock, Germany, from the 27-29th of March, and Gino D'Oca, assistant editor of Chemistry Central Journal, will be presenting a poster on open access publishing and chemistry. He will be delighted to meet anyone interested in open access to chemical research or those who simply wish to know more.
Chemistry Central will also be exhibiting and speaking at the American Chemical Society's spring conference in New Orleans (6-10 of April).
Posted by Gino D'Oca at 15:12 Comments (0)
Chemistry Central appoints two researchers to its editorial board
We are delighted to announce the following two appointments to the editorial board.
Dr. Muhammad A. Rauf, associate professor of physical chemistry at the United Arab Emirates university, UAE, has joined the editorial boards of environmental chemistry, nuclear/radiochemistry, and photochemistry.
Dr Rauf is involved in the study and application of advanced oxidation processes (AOPs) in the treatment of industrial effluents. The AOPs can be used to break chemicals down into less harmful substances, or completely destroy them under normal environmental conditions. He is interested in the analysis of the degraded species, and the interpretation of the associated kinetic data. Other interests include, the removal of selective metal ions/chemicals from solution using physical or chemical techniques such as adsorption and complexation, in addition to solute-solvent interactions.
Dr Plourde's research is focused on asymmetric synthetic methodology and its application in the synthesis of natural products, in addition to the isolation, characterisation and synthesis of compounds found in medicinal plants used by the First Nations of Northern British Columbia. Other interests include the medicinal chemistry of anti-cancer active compounds.
His support for open access to chemical research is also demonstrated by his acting as the guest editor of an upcoming special edition of Molecules.
Posted by Gino D'Oca at 12:23 Comments (0)
eChemistry project gets Microsoft funding
It was recently announced that Microsoft is to fund the two year eChemistry pilot project, whose aim will be to explore digital library technology in the hope of demonstrating the benefits to chemists of online, open access data. The work is a collaborative effort comprising chemists and computer scientists from eight bodies: Microsoft Research, PubChem, the Los Alamos National Laboratory, and the universities of Cambridge, Southampton (UK), Cornell, Indiana, and Penn state (USA).
Posted by Gino D'Oca at 12:15 Comments (0)
We are delighted to announce that Professor Bruno Pignataro of the department of physical chemistry at the university of
Palermo, Italy, has joined the editorial boards of nanotechnology and materials
chemistry.
Prof Pignataro's numerous research interests include the self-organisation of proteins and other biological materials, bidimensional
order in self-organised molecular monolayers, in addition to organic materials for use in plastic
electronic components such as transistors, photovoltaic cells, sensors and
biosensors. To study the chemical, mechanical, optical, and
electrical properties of nanoscale stuctures, his laboratory employs various
techniques, including advanced scanning probe methods and surface
spectroscopic techniques. He is a past
coordinator of the young chemists group of the Italian
chemical society, and chaired the first
European young chemist award in 2006.
He also acted as the
editor of the recently published book, 'Tomorrow's
Chemistry Today: Concepts in Nanoscience, Organic Materials and Environmental
Chemistry', which provides an overview of rising young scientists in the
fields of organic, materials and biochemistry.
Posted by Gino D'Oca at 14:23 Comments (0)