Chemistry Central Blog
Most accessed articles in January
Take a look at our ten most accessed papers for January.
The most accessed article last month describes the implementation of a “Chemically Aware” system to supplement the content management program, SharePoint. The system allows users to tag documents by drawing a structure and associating it with the related content. It also allows the user to search SharePoint software content and internal/external databases by carrying out substructure, similarity, SMILES, and IUPAC name searches.
The papers on the Open Babel toolkit and the CDK-Taverna project also remain well accessed – these are both important open source initiatives, and their continued popularity highlights the advantages of ‘openness’ in chemistry.
1. Making SharePoint(R) Chemically Aware(TM)
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. Predicting the mechanism of phospholipidosis
Robert Lowe, Hamse Y Mussa, Florian Nigsch, et al.
Journal of Cheminformatics 2012, 4:2 (26 January 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. New developments on the cheminformatics open workflow environment CDK-Taverna
Andreas Truszkowski, Kalai Vanii Jayaseelan, Stefan Neumann, et al.
Journal of Cheminformatics 2011, 3:54 (13 December 2011)
6. IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface
Yin Sun, Yan Huang, Feng Li, et al.
Chemistry Central Journal 2012, 6:2 (5 January 2012)
7. Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Noel M O'Boyle, Rajarshi Guha, Egon L Willighagen, et al.
Journal of Cheminformatics 2011, 3:37 (14 October 2011)
8. Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions
Peter Ertl, Ansgar Schuffenhauer
Journal of Cheminformatics 2009, 1:8 (10 June 2009)
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. Tracking antioxidant properties and color changes in low-sugar bilberry jam as effect of processing, storage and pectin concentration
Mariana-Atena Poiana, Ersilia Alexa, Constantin Mateescu
Chemistry Central Journal 2012, 6:4 (16 January 2012)
Posted by Bailey Fallon at 14:57 Comments (0)
Open Knowledge Foundation launches Panton Fellowships
The Open Knowledge Foundation has announced the launch of the Panton Fellowships. These will be awarded to scientists who actively promote open data in science, and who endorse the Panton Principles for making scientific data open.
The Panton Principles are a set of recommendations that address how best to make published data from scientific studies available for re-use, following the belief that “open data means better science”. The first draft of the Panton Principles was written in July 2009 by Peter Murray-Rust (part of the Journal of Cheminformatics Editorial Board), Cameron Neylon, Rufus Pollock and John Wilbanks, and was officially adopted in February 2010. The lack of a definition of 'open' was identified by the Blue Obelisk movement as a considerable stumbling block in advocating the release of scientific data as 'open data' but the launch of the Panton Principles provided a major step forward.
Panton Fellows will receive £8000 per annum to promote the concept of open data in science, and will be encouraged to explore practical solutions for making data open, facilitate discussions about the value of openness, and catalyse the open community.
Posted by Bailey Fallon at 16:29 Comments (0)
Journal of Cheminformatics accepted for Impact Factor tracking
We are pleased to announce that Journal of Cheminformatics has been accepted for tracking by Thomson Reuters and is expected to receive its first Impact Factor later this year.
This development comes after an exciting year in which the journal published its first thematic series of papers covering PubChem3D, RDF Technologies in Chemistry, and the Visions of a Semantic Molecular Future symposium, along with high profile articles on important cheminformatics tools, such as Open Babel and CDK-Taverna.
The journal’s standing in its field can be seen in the 2011 SCImago Journal Rank, which places it 4th out of 194 journals in the computer science applications category. Now that it has been accepted for Impact Factor tracking, we look forward to seeing even more growth and development over the coming years and we would like to thank our editors, authors and reviewers for their help in establishing Journal of Cheminformatics as a leading open access publication.
Posted by Bailey Fallon at 15:12 Comments (4)
Chemistry of Ageing: New thematic series for Chemistry Central Journal
We are pleased to announce a new thematic series for Chemistry Central Journal covering the Chemistry of Ageing.
Gerontology has traditionally been dominated by biological research groups. In recent years, the potential impact of chemical analysis and small molecule interventions has become widely recognised, and there are now a growing number of chemists undertaking ageing research. Research into ageing spans the full range chemistry. Advanced analytical and physical techniques are being used to observe age-related changes in living organisms. Equally, novel synthetic and medicinal chemistry is generating small molecule tools for the dissection of complex biological pathways, as well as potential life- and health-span extending therapeutics.
This thematic series, edited by Elizabeth Ostler from the University of Brighton, will cover:
- Glycation, oxidative stress and other degenerative processes
- Cellular senescence; mechanistic dissection and interventions
- Telomerase inhibitors and activators
- Small molecules with life-extending activity such as resveratrol and rapamycin
- Novel methods for mining complex cohort and life-course data
The first article in the series has already been published. In this study, Mark Bagley and colleagues at Cardiff University synthesised two diaminopyridine-based JNK inhibitors, and tested their effects on the proliferation and morphology of Werner syndrome fibroblasts in comparison to the widely used JNK inhibitor SP600125.
We welcome your contributions to this thematic series, and if you are interested in submitting a paper then please feel free to contact us for further information.
Posted by Bailey Fallon at 14:55 Comments (0)
Most accessed articles in December
Take a look at our ten most accessed papers for December.
The most popular article last month was published in Journal of Cheminformatics and covers new developments in the CDK-Taverna project. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through a combination of different open-source projects, and it recently migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture.
The most popular Chemistry Central Journal article last month was a study into the role of various forms of resveratrol in cancer proliferation. Resveratrol is a component of red wine that has been associated with various health benefits, and this paper compared the anti-proliferative effects of three isomers of resveratrol.
And the first publication reporting the features, implementation and validation of the open source toolkit Open Babel also continues to be very popular. 1. New developments on the cheminformatics open workflow environment CDK-Taverna
Andreas Truszkowski, Kalai Vanii Jayaseelan, Stefan Neumann, et al.
Journal of Cheminformatics 2011, 3:54 (13 December 2011)
2. Trans-, cis-, and dihydro-resveratrol: a comparative study
Natalia YU. Anisimova, Mikhail V. Kiselevsky, et al.
Chemistry Central Journal 2011, 5:88 (20 December 2011)3. 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)
4. MyChemise: A 2D drawing program that uses morphing for visualisation purposes
Jorg-Hubertus Wilhelm
Journal of Cheminformatics 2011, 3:53 (12 December 2011)5. 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)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. Molecular structure input on the web
Peter Ertl
Journal of Cheminformatics 2010, 2:1 (2 February 2010)
8. A highly efficient green synthesis of 1, 8-dioxo-octahydroxanthenes
Andivelu Ilangovan, Subramani Malayappasamy, Samraj Muralidharan, Sundaram Maruthamuthu
Chemistry Central Journal 2011, 5:81 (8 December 2011)
9. Development of validated stability-indicating chromatographic method for the determination of fexofenadine hydrochloride and its related impurities in pharmaceutical tablets
Hadir M Maher, Maha A Sultan, Ileana V Olah
Chemistry Central Journal 2011, 5:76 (3 December 2011)
10. Polyphosphates as a source of enhanced P fluxes in marine sediments overlain by anoxic waters: Evidence from 31P NMR
Poulomi Sannigrahi, Ellery Ingall
Geochemical Transactions 2005, 6:52 (22 June 2005)
Posted by Bailey Fallon at 16:34 Comments (0)
Chemistry Central at the MASC-11 meeting
Chemistry Central Journal will be attending the Macrocyclic and Supramolecular Chemistry (MASC-11) meeting taking place at the University of Bath from 19th–20th December.
The programme, organised by G Dan Pantoș and Chemistry Central Journal Section Editor Tony James, features a broad range of speakers, and will include three ‘Flash Sessions’ sponsored by Chemistry Central. The 9 researchers involved in these sessions will have just 8 minutes to deliver their talk, encouraging them to find imaginative ways to present their work. These Flash Sessions follow on from the very successful ‘Lightning Sessions’ that Chemistry Central organised at the Catalysis and Sensing for the Environment meeting earlier this year.
If you will be attending the meeting then we look forward to seeing you there, but those of you who can’t make it can still follow it on Facebook, or on Twitter using the hashtag #MASC11.
Posted by Bailey Fallon at 14:54 Comments (0)
New design for Chemistry Central
The Chemistry Central website has been updated with a new design, providing a clean and uncluttered look to take into account feedback from editors, authors, readers and reviewers.
In addition to the Chemistry Central portal, Chemistry Central Journal, Journal of Cheminformatics and Geochemical Transactions have also moved to the new design.
We encourage you to review and update your details and alert preferences, and explore the new site. Your feedback will help us further improve the new site's usability and usefulness. Key features include:
- A revamped homepage showcasing the most recent and popular published research including “Editor’s picks”
- My Chemistry Central – see the latest articles in your subject areas, and easily manage email preferences and stored searches
- My manuscripts – much improved display of the status of all your submitted/published manuscripts, and any that you are currently reviewing or have reviewed
- Institutional Member pages – these show all articles from a Member institution and an RSS feed makes it easy to stay up to date
- Advanced search – additional options for selecting and downloading search results
- Information pages – fully searchable, and with much simplified navigation, these pages tell you all you need to know about Chemistry Central
- Integrated blog and twitter feed – allowing you to keep up to date and in touch with Chemistry Central social media channels
- Expanded funding information pages allowing you to keep up with all the latest open access policy and funding news
- Detailed conference calendar – to keep track of the events that Chemistry Central will be attending in the coming year.
The new site is built on a modern technology platform that will serve as a solid foundation for many additional improvements which we plan to roll out in the coming months. We hope you like the new website, and look forward to receiving your feedback.
Posted by Bailey Fallon at 17:18 Comments (0)
Jean-Claude Bradley appointed co-Editor-in-Chief at Chemistry Central Journal
We are extremely pleased to announce the appointment of Jean-Claude Bradley as a co-Editor-in-Chief for Chemistry Central Journal.
Jean-Claude Bradley is an Associate Professor of Chemistry and E-Learning Coordinator for the College of Arts and Sciences at Drexel University, Philadelphia. He leads the UsefulChem project, a synthetic organic chemistry initiative started in the summer of 2005 to make the scientific process as transparent as possible by publishing all research work in real time to a collection of public blogs, wikis and other web pages. Jean-Claude coined the term Open Notebook Science to distinguish this approach from other more restricted forms of Open Science. In 2008 he created the Open Notebook Science Solubility Challenge to crowdsource the measurement of non-aqueous solubility.
Jean-Claude teaches undergraduate organic chemistry courses with most content freely available on public blogs, wikis, games, Second Life and audio and video podcasts. He has a Ph.D. in organic chemistry, and has published articles and obtained patents in the areas of synthetic and mechanistic chemistry, gene therapy, nanotechnology and scientific knowledge management.
Given Jean-Claude's experience and involvement in open science initiatives, we are delighted to have him on board to continue to take Chemistry Central Journal forward.
Posted by Bailey Fallon at 17:13 Comments (0)
A dramatic phenomenon in which light triggers the sudden rupture of fatty acid vesicles has been observed in a primitive cell membrane model. The findings, published by Nobel Laureate Jack Szostak et al. in Journal of Systems Chemistry, could lead to applications such as targeted drug delivery, and the controlled deposition of functionalized nanoparticles in microfluidic devices.
Fatty acid vesicles are commonly used as models of primitive cell membranes in studies of abiogenesis. While studying large dye-containing oleate vesicles, the authors found that exposure to intense illumination caused them to suddenly explode, releasing their encapsulated dye along with smaller internal vesicles. They propose a mechanism in which reactive oxygen species (ROS) are generated from the dye upon illumination. These ROS oxidize the internal buffer, leading to an increase in internal osmotic pressure, and ultimately, vesicle rupture.
This unexpected phenomenon could have a number of practical applications, including its use in cancer therapy. “A major question in treating cancer is how to localize the release of cytotoxic drugs to target tumors, thus reducing systemic toxicity” explains Szostak. “By delivering a drug such as a chemotherapeutic agent through photoactivation, exploding vesicles may be used to localize drug release and strengthen the effectiveness of cancer treatments.”
Posted by Bailey Fallon at 15:04 Comments (0)
Most accessed articles in November
Take a look at our ten most accessed papers for November.
Our most popular paper last month was a Commentary by Sharon Haynie et al., published as part of the Women in Chemistry thematic series in Chemistry Central Journal. One of the goals of the International Year of Chemistry, which has been taking place over the past year, has been to celebrate the achievements of women in science. This Commentary recognizes these achievements by describing the personal journeys of six women pursuing careers in chemistry
1. Reflections on the journey: six short stories
Sharon L Haynie, Amber S Hinkle, Nancy L Jones, et al.
Chemistry Central Journal 2011, 5:69 (7 November 2011)
2. Correlation between Fischer-Tropsch catalytic activity and composition of catalysts
Sardar Ali, Noor Mohd Zabidi, Duvvuri Subbarao
Chemistry Central Journal 2011, 5:68 (3 November 2011)
3. 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)
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. 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)
6. 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)
7. Synthesis and characterization of novel 2,2'-bipyrimidine fluorescent derivative for protein binding
Vikas S. Padalkar, Vikas S. Patil, N. Sekar
Chemistry Central Journal 2011, 5:72 (9 November 2011)
8. Automated annotation of chemical names in the literature with tunable accuracy
Jun D. Zhang, Lewis Y. Geer, Evan E. Bolton, Stephen H. Bryant
Journal of Cheminformatics 2011, 3:52 (22 November 2011)
9. Hydrolysis optimization and characterization study of preparing fatty acids from Jatropha curcas seed oil
Jumat Salimon, Bashar Abdullah, Nadia Salih
Chemistry Central Journal 2011, 5:67 (1 November 2011)
10. Detection of stanozolol in environmental waters using liquid chromatography tandem mass spectrometry
Nawed IK Deshmukh, James Barker, Andrea Petroczi, Declan P Naughton
Chemistry Central Journal 2011, 5:63 (14 October 2011)
Posted by Bailey Fallon at 14:42 Comments (0)
Poster prize winners at Systems Chemistry III
We are pleased to announce the poster prize winners for the Systems Chemistry III conference, which was held in Crete, Greece last month. The conference was sponsored by Journal of Systems Chemistry and many of the presentations were delivered by Editorial Board Members, including co-Editors-in-Chief Günter von Kiedrowski and Sijbren Otto.
Prizes were awarded for the following four posters:
Mirror Symmetry Breaking at Interfaces: Glycine and Alpha-Amino Acids
Celia Blanco, Centro de Astrobiología (CSIC-INTA), Spain
A mathematical model of the experimentally established mechanisms responsible for the symmetry breaking transition observed in chiral crystallization experiments was presented.
How “Mutations” Affect the Self-Replication of Peptide Functionalised Macrocycles
Mathieu Colomb-Delsuc, Rijksuniversiteit Groningen, Netherlands
New dynamic combinatorial libraries were made from dithiol building blocks functionalized with a peptide chain designed to form beta-sheets.
Two Different Template Replicators Coexisting in the Same Protocell: Stochastic Simulation of an Extended Chemoton Model
Anna Fedor, Eötvös Lorand University of Sciences, Hungary
The minimal cell model, chemoton, and an extended version with two competing template cycles were implemented. The stoichiometric coupling of components in the chemoton ensures that these templates coexist, providing an alternative solution to Eigen's paradox.
Self-Propagating Molecular-Based Assemblies
Leila Motiei, Weizmann Institute of Science, Israel
An investigation into the formation and properties of self-propagating molecular assemblies, including electrochromic behavior, photovoltaic performance, charge transfer properties and selective permeation of small molecules.
Posted by Bailey Fallon at 11:00 Comments (0)
7th German Conference on Chemoinformatics
The 7th German Conference on Chemoinformatics is being held in Goslar Germany next week from 6th-8th November, and once again Journal of Cheminformatics will be the conference publishing partner and poster session sponsor.
The conference spans a wide range of contributions related to computer aided processes in chemistry, and to chemical information, and this year’s meeting will open with a lecture from Editorial Board Member Johann Gasteiger (University of Erlangen-Nürnberg) entitled ‘25 Years of CIC – Achievements and Future Goals’. The following two days are made up of sessions covering cheminformatics and drug discovery, computational materials science and nanotechnology, chemical information, patents and databases, and molecular modeling, as well as a poster session and exhibition.
The abstracts for 24 oral presentations and 43 posters from last year’s meeting were published in Journal of Cheminformatics earlier this year.
Posted by Bailey Fallon at 16:04 Comments (0)
Most accessed articles in October
Take a look at our ten most accessed papers for October.
Six of the top ten papers cover various forms of ‘openness’ in science, with topics including open access (see Openness as infrastructure), open bibliography (see Open Bibliography for Science, Technology, and Medicine) and open source software (see Open Babel: An open chemical toolbox). Many of these papers were published as part of the ‘Visions of a Semantic Future’ thematic series in Journal of Cheminformatics, which looks at the application of semantic technologies to molecular science, and how this will change the way science is published in the future.
It is encouraging to see that the most popular articles in the last month are those that look at publishing science openly, as this ties in with our view that open access to research is essential to ensure the rapid and efficient communication of research findings.
1. Openness as infrastructure
John Wilbanks
Journal of Cheminformatics 2011, 3:36 (14 October 2011)
2. Linked open drug data for pharmaceutical research and development
Matthias Samwald, Anja Jentzsch, Christopher Bouton, et al.
Journal of Cheminformatics 2011, 3:19 (16 May 2011)3. 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)
4. Open Bibliography for Science, Technology, and Medicine
Richard Jones, Mark MacGillivray, Peter Murray-Rust, et al.
Journal of Cheminformatics 2011, 3:47 (14 October 2011)5. Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Noel M O'Boyle, Rajarshi Guha, Egon L Willighagen, et al.
Journal of Cheminformatics 2011, 3:37 (14 October 2011)
6. Semantic science and its communication - a personal view
Peter Murray-Rust
Journal of Cheminformatics 2011, 3:48 (14 October 2011)7. 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)
8. Detection of stanozolol in environmental waters using liquid chromatography tandem mass spectrometry
Nawed I K Deshmukh, James Barker, Andrea Petroczi, Declan P Naughton
Chemistry Central Journal 2011, 5:63 (14 October 2011)
9. CML: Evolution and Design
Peter Murray-Rust, Henry S Rzepa
Journal of Cheminformatics 2011, 3:44 (14 October 2011)10. 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)
Posted by Bailey Fallon at 15:26 Comments (0)
Visions of a semantic molecular future
Journal of Cheminformatics has just published its latest thematic series – Visions of a Semantic Molecular Future. The series of papers originates from a symposium held earlier this year to celebrate the career of Peter Murray-Rust, Reader at the Unilever Centre for Molecular Science Informatics, University of Cambridge, and a strong advocate of open access and open data. With contributions from several of the speakers, as well as members of the Murray-Rust group, the papers address the application of semantic technologies to molecular science, and look at where we might be heading in the future.
Amonst the many notable contributions in the series is the article on ‘Open Bibliography for Science, Technology, and medicine’. It presents BibJSON, a simple structured text data format suitable for serialisation and storage of large quantities of bibliographic data, and encourages the development of improved methods of processing the wealth of information and knowledge embedded in bibliographic data. In the interests of embracing the technologies that the article describes we have chosen on this occasion to publish it in HTML format only. Presenting it as a PDF would have meant losing the proper context of the original document and reducing the impact of the research.
Another key paper describes the work carried out by the Blue Obelisk movement over the last five years, with a discussion of the current progress and future challenges in Open Data, Open Standards, and Open Source in chemistry.
In addition to the papers that describe the various software and tools that are being used as part of the growing Semantic Web, several commentary-type articles by Henry Rzepa, Cameron Neylon, John Wilbanks and Dan Zaharevitz provide a much broader look at scholarly publishing. They reach similar conclusions about the benefits of openness and should be of interest not only to the cheminformatics community, but to those working in all areas of science.
Posted by Bailey Fallon at 17:16 Comments (0)