Chemistry Central Blog
Multivariate Analysis and Chemometry to Cultural Heritage and Environment
Chemistry Central Journal has just published its latest supplement ‘CMA4CH 2010: Multivariate Analysis and Chemometry to Cultural Heritage and Environment’. The collection of papers features a representative selection of research that was presented at the CMA4CH 2010 meeting held in Taormina, Italy.
Research into cultural heritage and the environment produces large amounts of data, but classical data analysis methods can lead to much of this information being lost. Chemometrics and multivariate analysis represent newer methods of dealing with this data, and the application of these techniques was the focus of the conference.
The 11 papers that make up the supplement went through a non-standard peer review process consisting of three stages, the first to check consistency and quality balance, the second to check chemical/physical aspects, and the third to check multivariate and chemometry content. “Although slow, this method allowed us to obtain a very homogeneous set of papers and, I hope, papers of a high scientific content” explains Giovanni Visco, the meeting coordinator and supplement editor.
The supplement coincides with publication of the ‘Chemistry and materials for cultural heritage’ thematic series, which published its first articles in March. These papers cover techniques to analyse, understand and prevent deterioration of cultural objects, and should be relevant to readers of the CMA4CH 2010 supplement. Further papers will be added to the thematic series over the coming months.
Posted by Bailey Fallon at 11:22 Comments (0)
Supplement from the 7th German Conference on Chemoinformatics
Journal of Cheminformatics has published the meeting abstracts from the 7th German Conference on Chemoinformatics, which took place in Goslar, Germany last November.
Journal of Cheminformatics is the official publishing partner of the conference, and the 2011 meeting is the third consecutive year that the journal has been involved. The meeting also marked the 25th anniversary of the Chemistry-Information-Computers division of the German Chemical Society, which was reflected on in Johann Gasteiger’s talk, ‘25 years of CIC – achievements and future goals’.
Other topics that the meeting focussed on were:
- Chemoinformatics and Drug Discovery
- Chemical Information, Patents and Databases
- Molecular Modeling
- Computational Materials Science and Nanotechnology
The abstracts from this, as well as the previous two meetings, are freely available via the Journal of Cheminformatics website.
Posted by Bailey Fallon at 15:09 Comments (0)
Most accessed articles in April
Take a look at our ten most accessed papers for April.
Among the most popular papers published last month is a research article from Journal of Cheminformatics co-Editor-in-Chief Christoph Steinbeck and colleagues. The paper analyzes the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions, and goes on to compare these patterns to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology.
Also popular was an article from Mark Bagley and colleagues published as part of the Chemistry of Ageing issue in Chemistry Central Journal, which describes the microwave-assisted synthesis of a series of hydrazinyl thiazolyl coumarins. Several of the compounds displayed significant radical-scavenging ability, making them promising leads for further development and optimization.
1. Making SharePoint® Chemically Aware™
Kartik Tallapragada, Joseph Chewning, David Kombo, Beverly Ludwick
Journal of Cheminformatics 2012, 4:1 (12 January 2012)
2. Cacao seeds are a "Super Fruit": A comparative analysis of various fruit powders and products
Stephen J Crozier, Amy G Preston, Jeffrey W Hurst, et al.
Chemistry Central Journal 2011, 5:5 (7 February 2011)
3. Structure-based classification and ontology in chemistry
Janna Hastings, Despoina Magka, Colin Batchelor, et al.
Journal of Cheminformatics 2012, 4:8 (5 April 2012)
4. CheS-Mapper - Chemical Space Mapping and Visualization in 3D
Martin Gütlein, Andreas Karwath, Stefan Kramer
Journal of Cheminformatics 2012, 4:7 (17 March 2012)
5. Toward a general theory of evolution: Extending Darwinian theory to inanimate matter
Addy Pross
Journal of Systems Chemistry 2011, 2:1 (7 June 2011)
6. Different extraction methods of biologically active components from propolis: a preliminary study
Boryana Trusheva, Dorina Trunkova, Vassya Bankova
Chemistry Central Journal 2007, 1:13 (7 June 2007)
7. Open Babel: An open chemical toolbox
Noel M O'Boyle, Michael Banck, Craig A James, et al.
Journal of Cheminformatics 2011, 3:33 (7 October 2011)
8. Rapid determination of natural steroidal hormones in saliva for the clinical diagnoses
Jin-Aa Oh, Ho-Sang Shin
Chemistry Central Journal 2012, 6:22 (28 March 2012)
9. Synthesis and antibacterial activity against ralstonia solanacearum for novel hydrazone derivatives containing a pyridine moiety
Jian Wu, Shenghong Kang, Baoan Song, et al.
Chemistry Central Journal 2012, 6:28 (7 April 2012)
10. Microwave-assisted synthesis and antioxidant properties of hydrazinyl thiazolyl coumarin derivatives
Hasnah Osman, Afsheen Arshad, Chan K Lam, Mark C Bagley
Chemistry Central Journal 2012, 6:32 (17 April 2012)
Posted by Bailey Fallon at 11:44 Comments (0)
Roles for chemistry in the world's energy problems
Chemistry has a vital role to play in meeting today’s energy demands as well as in shaping energy policy. These contributions are explored in the latest supplement to be published in Chemistry Central Journal, ‘Roles for chemistry in the world's energy problems’.
The articles originate from a course organised by Editor-in-Chief Stephen Berry along with George Tolley at the University of Chicago. The participants worked in groups to prepare a report on a chosen topic around the role of chemistry in energy and energy policy, and the resulting six papers cover a range of important issues, including solar power, biofuels and smart meters.
A preface to the supplement highlights the key functions that the papers serve. The first, in keeping with Chemistry Central Journal’s aim to encompass all areas of chemistry, is to highlight important areas where chemistry may not be the only contributing subject. “Chemistry plays an integral role in the acquisition, generation, distribution and efficient use of energy” explains Prof. Berry, “but its role is only fully meaningful when chemistry’s contributions are integrated with those of other sciences such as climatology, and with economics, sociology and political decision-making.
The second, even more importantly, is based around education. Students were required to work together in interdisciplinary teams, and therefore needed to coherently explain their field while understanding concepts from different subjects. Furthermore, the reports were presented in an environment that encouraged questions and critical comments – some of the basic principles of effective scientific communication.
Readers are encouraged to leave their own comments on these, or any other articles in the journal.
Posted by Bailey Fallon at 11:21 Comments (0)
Chemical consequences of cutaneous photoageing
Human skin undergoes a number of age-related changes, such as wrinkle formation and loss of elasticity, but the onset of these changes is accelerated by exposure to ultraviolet (UV) radiation. Most investigations have concentrated on the cell as both a target for and mediator of UV-induced photoageing, but recent studies have shown that key proteins in the extracellular matrix (ECM) may be more directly susceptible to UV-induced damage than previously thought.
The latest review published in Chemistry Central Journal examines the experimental evidence for UV-induced, as opposed to cell-mediated, photodamage of normally long lived dermal proteins. Michael Sheratt and colleagues from The University of Manchester discuss the composition of healthy skin, the effects of UV exposure on the skin, and the evidence that UV radiation directly and differentially degrades the biomolecules found in skin. They go on to explore the potential for amino acid composition alone (as opposed to high order structures) to predict the susceptibility of key ECM proteins to direct and indirect degradation.
The review is the latest article to be published in the Chemistry of Ageing thematic issue, which also covers:
- Synthesis and antioxidant properties of a range of coumarins with radical-scavenging ability
- Analysis of age-related changes in mucosal serotonin transmission in the ileum
- Glyoxal-induced senescence in telomerase-immortalized human mesenchymal stem cells
- The effects of two new JNK inhibitors on the proliferation and morphology of Werner syndrome fibroblasts
Posted by Bailey Fallon at 16:20 Comments (0)
Two new article types for Chemistry Central Journal
Chemistry Central Journal has introduced two new article types – Short Reports and Perspectives – in order to provide authors with greater choice when submitting their manuscripts.
Short Reports are ideally suited for small scale studies that extend previously published work, but which may be too limited in scope for publication as a full research article. Short Reports will also be suitable for reporting additional data and confirmatory results in other settings.
Perspectives are designed to highlight important issues and provoke discussion around a particular topic. While similar in nature to Commentary articles, Perspectives are more forward looking, offering new hypotheses, alternative interpretations of existing work, or presenting new proposals for tackling existing problems. Journal of Systems Chemistry, which is also published by Chemistry Central, has published several Perspectives since its launch two years ago
You can submit Short Reports, Perspectives, or any of our other article types, via our online submission system.
Posted by Bailey Fallon at 12:25 Comments (0)
52 Nobel laureates endorse FRPAA
52 Nobel Laureates have signed an open letter to the US Congress expressing their support for the Federal Research Public Access Act (FRPAA). The signatories include 22 chemists, among which are the most recent Nobel Prize winner, Daniel Shechtman, and Chemistry Central Journal Editorial Board Member Robert Curl.
The letter explains that “broad dissemination of research results is fundamental to the advancement of knowledge”, and if passed, FRPAA would ensure this by mandating “free online public access” to any federally funded research.
Previous versions of FRPAA were introduced to Congress in 2006 and 2009, but the most recent version was introduced in February 2012, following the controversial Research Works Act (RWA). While FRPAA is seeking to improve access to research outputs by building on established public access policies, RWA would have prohibited open access mandates for federally funded research. Support for RWA was withdrawn on February 27th 2012.
Posted by Bailey Fallon at 16:13 Comments (0)
LabArchives and BioMed Central: a new platform for publishing scientific data
As part of its commitment to reproducible research and transparency, BioMed Central has partnered with LabArchives to work towards making datasets supporting peer-reviewed publications available and permanently linked to online publications as Open Data.
LabArchives is an Electronic Lab Notebook that can be used by scientists to store, organize, share and publish their laboratory data. As part of the partnership with BioMed Central, which also extends to Chemistry Central’s journals, authors are entitled to an enhanced free version of LabArchives. This ‘BioMed Central Edition’ of the software offers 100 MB of storage (four times as much as the standard free edition), as well as integrated manuscript submission to BioMed Central journals, and important open data publishing features.
With large datasets becoming increasingly common in scientific publishing, LabArchives allows authors to upload files that cannot be easily accommodated within the journal articles, or for which standard repositories do not exist. In addition, the ability to assign DOIs to the datasets facilitates citation within the article.
For more information about BioMed Central’s partnership with LabArchives, please visit the BMC blog.
Posted by Bailey Fallon at 15:34 Comments (0)
Most accessed articles in March
Take a look at our ten most accessed papers for March.
The most popular paper published last month was a Journal of Cheminformatics paper describing an open source 3D molecular viewer known as Ches-Mapper. Analyzing chemical datasets is an important yet challenging task for researchers aiming to understand structure–property relationships. Visualization tools can help to better comprehend the underlying correlations, and CheS-Mapper is a tool that divides large datasets into clusters of similar compounds and consequently arranges them in 3D space.1. Toward a general theory of evolution: Extending Darwinian theory to inanimate matter
Addy Pross
Journal of Systems Chemistry 2011, 2:1 (7 June 2011)2. Cacao seeds are a "Super Fruit": A comparative analysis of various fruit powders and products
Stephen J Crozier, Amy G Preston, Jeffrey W Hurst, et al.
Chemistry Central Journal 2011, 5:5 (7 February 2011)3. CheS-Mapper - Chemical Space Mapping and Visualization in 3D
Martin Gutlein, Andreas Karwath, Stefan Kramer
Journal of Cheminformatics 2012, 4:7 (17 March 2012)4. Open Babel: An open chemical toolbox
Noel M O'Boyle, Michael Banck, Craig A James, et al.
Journal of Cheminformatics 2011, 3:33 (7 October 2011)
5. Improving integrative searching of systems chemical biology data using semantic annotation
Bin Chen, Ying Ding, David J Wild
Journal of Cheminformatics 2012, 4:6 (8 March 2012)
6. The Effect of the CO32- to Ca2+ Ion Activity Ratio on Calcite Precipitation Kinetics and Sr2+ partitioning
Tsigabu A Gebrehiwet, George D Redden, Yoshiko Fujita, et al.
Geochemical Transactions 2012, 13:1 (26 January 2012)7. Different extraction methods of biologically active components from propolis: a preliminary study
Boryana Trusheva, Dorina Trunkova, Vassya Bankova
Chemistry Central Journal 2007, 1:13 (7 June 2007)
8. Rapid and mobile determination of alcoholic strength in wine, beer and spirits using a flow-through infrared sensor
Dirk W Lachenmeier, Rolf Godelmann, Markus Steiner, et al.
Chemistry Central Journal 2010, 4:5 (23 March 2010)
9. Ficaria verna Huds. extracts and their beta-cyclodextrin supramolecular systems
Nicoleta G Hadaruga
Chemistry Central Journal 2012, 6:16 (5 March 2012)
10. Predicting the mechanism of phospholipidosis
Robert Lowe, Hamse Y Mussa, Florian Nigsch, et al.
Journal of Cheminformatics 2012, 4:2 (26 January 2012)
Posted by Bailey Fallon at 11:48 Comments (0)
Chemistry Central at the spring ACS meeting
Chemistry Central will be at the Spring ACS Meeting in San Diego, California next week. You can find us at booth 419 and we’ll be giving away free T-shirts throughout the exhibition. Please feel free to drop by to pick one up and find out about the latest developments at
Chemistry Central.
Readers of Journal of Systems Chemistry should find several parts of the technical program of interest. A session on Systems Chemical Biology on the Tuesday has been organised by Tudor Oprea, University of New Mexico, and Jan Kuras, Chemistry Central publisher, covering a range of "Systems" Approaches in Chemistry and Biology Research. In addition, ‘From Geochemistry to Biochemistry and the Origin of Life’ features presentations on a number of topics in systems chemistry and includes talks from Journal of Systems Chemistry Board Members Jack Szostak, Donna Blackmond and Gerald Joyce.
Several Editorial Board Members for Journal of Cheminformatics will also be presenting during the conference. The InChI Symposium will include talks from Antony Williams and Martin Walker, and Rajashi Guha has organised the CINFlash session, where speakers have just a few minutes to present their research. Co-Editor-in-Chief David Wild will present ‘Assessing drug target association using semantic linked data’ during the Drug Polypharmacology Prediction and Design session and will also be speaking in the Systems Chemical Biology session.
Posted by Bailey Fallon at 14:41 Comments (0)
Computational Chemistry Highlights launched
Computational Chemistry Highlights, a new overlay journal that identifies important contributions to the field of computational and theoretical chemistry, was launched last month.
An overlay journal is a type of open access journal where the content is derived from existing public domain sources, such as open access repositories and preprint servers. Content for Computational Chemistry Highlights, will be selected by their Editorial Board, which features Chemistry Central Journal Board Member Steven Bachrach (Trinity University, USA). They will 
select papers from the previous 1–2 years of research based on their own reading of the literature. Seven articles have been published to date, including a 2011 paper from Journal of Cheminformatics, Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method.
Computational Chemistry Highlights is a free resource and represents an interesting example of the new ways in which chemistry is communicated.
Posted by Bailey Fallon at 14:59 Comments (0)
Most accessed articles in February
Take a look at our ten most accessed papers for February.
The most accessed paper last month was a Journal of Systems Chemistry Perspective by Addy Pross, which aims to explain the emergence of life by extending Darwinian theory to inanimate matter. The Perspective was covered by the popular science magazine, Discover, leading to a surge in interest.
Also of interest was a software article published in Journal of Cheminformatics, which describes an open source chemical spreadsheet that runs within Microsoft Excel and can be used on sheets containing hundreds of thousands of compounds without compromising normal performance.1. Toward a general theory of evolution: Extending Darwinian theory to inanimate matter
Addy Pross
Journal of Systems Chemistry 2011, 2:1 (7 June 2011)2. Cacao seeds are a "Super Fruit": A comparative analysis of various fruit powders and products
Stephen J Crozier, Amy G Preston, Jeffrey W Hurst, et al.
Chemistry Central Journal 2011, 5:5 (7 February 2011)
3. LICSS - A chemical spreadsheet in Microsoft Excel
Kevin R Lawson, Jonty Lawson
Journal of Cheminformatics 2012, 4:3 (2 February 2012)4. Predicting the mechanism of phospholipidosis
Robert Lowe, Hamse Y Mussa, Florian Nigsch, et al.
Journal of Cheminformatics 2012, 4:2 (26 January 2012)
5. Blind trials of Computer-Assisted Structure Elucidation software
Arvin Moser, Mikhail E Elyashberg, Antony J Williams, et al.
Journal of Cheminformatics 2012, 4:5 (9 February 2012)
6. Novel spectrophotometric method for determination of cinacalcet hydrochloride via derivatization with 1,2-naphthoquinone-4-sulphonate
Ibrahim A Darwish, Mona M Al-Shehri, Manal A El-Gendy
Chemistry Central Journal 2012, 6:11 (3 February 2012)
7. A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space
Narender Singh, Hongmao Sun, Sidhartha Chaudhury, et al.
Journal of Cheminformatics 2012, 4:4 (8 February 2012)
8. Comparison of sterols and fatty acids in two species of Ganoderma
Guang-ping Lv, Jing Zhao, Jin-ao Duan, et al.
Chemistry Central Journal 2012, 6:10 (31 January 2012)9. Different extraction methods of biologically active components from propolis: a preliminary study
Boryana Trusheva, Dorina Trunkova, Vassya Bankova
Chemistry Central Journal 2007, 1:13 (7 June 2007)
10. Evaluation of phenolic contents and antioxidant activity of various solvent extracts of Sonchus asper (L.) Hill
Rahmat Ali Khan, Muhammad Rashid Khan, Sumaira Sahreen, et al.
Chemistry Central Journal 2012, 6:12 (6 February 2012)
Posted by Bailey Fallon at 15:10 Comments (0)
Improved equation display for Chemistry Central articles using MathJax
Articles published in Chemistry Central journals will now benefit from improved equation display by implementing MathJax, an open source JavaScript display engine for mathematics.
In the past, equations have been rendered as graphics, which suffer from pixelation when scaling the page. However, equations rendered using MathJax are scaled at the same zoom rate as the text, and can also be copied and pasted into other applications.
More information about MathJax can be found on the BioMed Central blog, and to see how equations are now rendered using MathJax, take a look at the following Chemistry Central articles:
Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain
Abrar Hussain, Peter E Shaw, Jonathan D Hirst
Journal of Cheminformatics 2011, 3:49 (1 November 2011)
Experimental Study of Cement - Sandstone/Shale - Brine - CO2 Interactions
Susan A Carroll, Walt W McNab, Sharon C Torres
Geochemical Transactions 2011, 12:9 (11 November 2011)
Posted by Bailey Fallon at 12:17 Comments (2)
10th Anniversary of the Budapest Open Access Initiative
Today marks ten years since the launch of the Budapest Open Access Initiative (BOAI).
The purpose of the BOAI was to accelerate progress in the international effort to make research articles in all academic fields freely available on the internet. Central to this was a clear definition of what constitutes ‘open access’:
“By ‘open access’ to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.”
Since the Budapest Declaration was published, open access publishing has experienced rapid growth. The Directory of Open Access Journals now lists close to 7500 journals, compared to just 33 journals ten years ago, and it is expanding at a rate of almost 3 journals per day. With a far greater awareness of open access today, and with funders increasingly requiring open access to research and data, we look forward to seeing even more growth over the next ten years.
Posted by Bailey Fallon at 14:52 Comments (0)
The Eightfold Path to non-enzymatic RNA replication
The principal question in studies of abiogenesis centres on how the RNA World emerged from the prebiotic chemistry of the early Earth. Traditional models are based on the concept of an RNA replicase, but in the latest Perspective to be published in Journal of Systems Chemistry, Jack Szostak discusses the growing evidence that this process may have been chemically, rather than enzymatically driven.
The RNA World hypothesis proposes that current DNA-based life was predated by life based on RNA. While considerable evidence exists to support this model, there is still a lack of understanding regarding how cycles of template-directed RNA replication could occur. The original RNA World model was based around RNA-mediated catalysis but experimental demonstrations of RNA-catalyzed RNA copying have revealed significant barriers that would need to be overcome for this to be achieved.
“In light of [these] problems, I suggest that it is worthwhile to revisit the much earlier model of chemical (i.e., non-enzymatic) RNA replication”, explains Szostak, who identifies 8 issues that must be overcome in an experimental demonstration of RNA replication. While these perceived difficulties may make chemically-driven RNA replication seem even more challenging than the enzymatic process, Szostak’s Perspective addresses each one in turn, presenting recent evidence that shows there are potential solutions to all of these problems.
“Although a great deal of experimental work must yet be done, all of the major apparent stumbling blocks on the path to RNA replication appear to be at least potentially amenable to fairly simple solutions”.
Posted by Bailey Fallon at 10:25 Comments (0)