Data Journals: Incentivizing Data Access and Documentation Within the Scholarly Communication System
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Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al. -
Open Data, Open Source and Open Standards in Chemistry: the Blue Obelisk five Years On
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk ¯ve years on Noel M O'Boyle¤1 , Rajarshi Guha2 , Egon L Willighagen3 , Samuel E Adams4 , Jonathan Alvarsson5 , Richard L Apodaca6 , Jean-Claude Bradley7 , Igor V Filippov8 , Robert M Hanson9 , Marcus D Hanwell10 , Geo®rey R Hutchison11 , Craig A James12 , Nina Jeliazkova13 , Andrew SID Lang14 , Karol M Langner15 , David C Lonie16 , Daniel M Lowe4 , J¶er^omePansanel17 , Dmitry Pavlov18 , Ola Spjuth5 , Christoph Steinbeck19 , Adam L Tenderholt20 , Kevin J Theisen21 , Peter Murray-Rust4 1Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, Co. Cork, Ireland 2NIH Center for Translational Therapeutics, 9800 Medical Center Drive, Rockville, MD 20878, USA 3Division of Molecular Toxicology, Institute of Environmental Medicine, Nobels vaeg 13, Karolinska Institutet, 171 77 Stockholm, Sweden 4Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lens¯eld Road, CB2 1EW, UK 5Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden 6Metamolecular, LLC, 8070 La Jolla Shores Drive #464, La Jolla, CA 92037, USA 7Department of Chemistry, Drexel University, 32nd and Chestnut streets, Philadelphia, PA 19104, USA 8Chemical Biology Laboratory, Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA 9St. Olaf College, 1520 St. Olaf Ave., North¯eld, MN 55057, USA 10Kitware, Inc., 28 Corporate Drive, Clifton Park, NY 12065, USA 11Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA 12eMolecules Inc., 380 Stevens Ave., Solana Beach, California 92075, USA 13Ideaconsult Ltd., 4.A.Kanchev str., So¯a 1000, Bulgaria 14Department of Engineering, Computer Science, Physics, and Mathematics, Oral Roberts University, 7777 S. -
On the Redundancy of Natural Products Public Databases and Where to Find Data in 2020 - a Review on Natural Products Databases
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 25 December 2019 doi:10.20944/preprints201912.0332.v1 On the redundancy of natural products public databases and where to find data in 2020 - a review on natural products databases Dr. Maria Sorokina (ORCID 0000-0001-9359-7149) Prof. Dr. Christoph Steinbeck (ORCID 0000-0001-6966-0814) Institute for Inorganic and Analytical Chemistry Friedrich-Schiller-University Lessingstr. 8 07743 Jena Abstract Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date. -
Cheminformatics for Genome-Scale Metabolic Reconstructions
CHEMINFORMATICS FOR GENOME-SCALE METABOLIC RECONSTRUCTIONS John W. May European Molecular Biology Laboratory European Bioinformatics Institute University of Cambridge Homerton College A thesis submitted for the degree of Doctor of Philosophy June 2014 Declaration This thesis is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation is not substantially the same as any I have submitted for a degree, diploma or other qualification at any other university, and no part has already been, or is currently being submitted for any degree, diploma or other qualification. This dissertation does not exceed the specified length limit of 60,000 words as defined by the Biology Degree Committee. This dissertation has been typeset using LATEX in 11 pt Palatino, one and half spaced, according to the specifications defined by the Board of Graduate Studies and the Biology Degree Committee. June 2014 John W. May to Róisín Acknowledgements This work was carried out in the Cheminformatics and Metabolism Group at the European Bioinformatics Institute (EMBL-EBI). The project was fund- ed by Unilever, the Biotechnology and Biological Sciences Research Coun- cil [BB/I532153/1], and the European Molecular Biology Laboratory. I would like to thank my supervisor, Christoph Steinbeck for his guidance and providing intellectual freedom. I am also thankful to each member of my thesis advisory committee: Gordon James, Julio Saez-Rodriguez, Kiran Patil, and Gos Micklem who gave their time, advice, and guidance. I am thankful to all members of the Cheminformatics and Metabolism Group. -
Life Initiated from Two Genes, As Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems
life Article A Hypothesis: Life Initiated from Two Genes, as Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems Kunio Kawamura Department of Human Environmental Studies, Hiroshima Shudo University, 1-1-1, Ozuka-higashi, Asaminami-ku, Hiroshima 731-3195, Japan; [email protected]; Tel.: +81-82-830-1946 Academic Editor: David Deamer Received: 7 June 2016; Accepted: 25 July 2016; Published: 2 August 2016 Abstract: RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life. For instance, an RNA-based life-like system should possess enough stability to resist environmental perturbations, by developing a cell-like compartment, for instance. Here, a conceptual viewpoint is summarized to provide a realistic life-like system that is compatible with the primitive Earth environment and the capabilities of RNA molecules. According to the empirical and conceptual analysis, I propose the hypothesis that the first life-like system could have initiated from only two genes. Keywords: first genes; metabolism; information flow; RNA world; hydrothermal environments; kinetic model; definition of life; Hadean Earth environments 1. -
Journal of Molecular Biology
JOURNAL OF MOLECULAR BIOLOGY AUTHOR INFORMATION PACK TABLE OF CONTENTS XXX . • Description p.1 • Audience p.2 • Impact Factor p.2 • Abstracting and Indexing p.2 • Editorial Board p.2 • Guide for Authors p.6 ISSN: 0022-2836 DESCRIPTION . Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology Cell cycle, cell growth, cell differentiation Cell death, autophagy Cell signaling and regulation Chemical biology Computational biology, in combination with experimental studies DNA replication, repair, and recombination Development, regenerative biology, mechanistic and functional studies of stem cells Epigenetics, chromatin structure and function Gene expression Receptors, channels, and transporters Membrane processes Cell surface proteins and cell adhesion Methodological advances, both experimental and theoretical, including databases Microbiology, virology, and interactions with the host or environment Microbiota mechanistic and functional studies Nuclear organization Post-translational modifications, proteomics Processing and function of biologically -
States of Origin: Influences on Research Into the Origins of Life
COPYRIGHT AND USE OF THIS THESIS This thesis must be used in accordance with the provisions of the Copyright Act 1968. Reproduction of material protected by copyright may be an infringement of copyright and copyright owners may be entitled to take legal action against persons who infringe their copyright. Section 51 (2) of the Copyright Act permits an authorized officer of a university library or archives to provide a copy (by communication or otherwise) of an unpublished thesis kept in the library or archives, to a person who satisfies the authorized officer that he or she requires the reproduction for the purposes of research or study. The Copyright Act grants the creator of a work a number of moral rights, specifically the right of attribution, the right against false attribution and the right of integrity. You may infringe the author’s moral rights if you: - fail to acknowledge the author of this thesis if you quote sections from the work - attribute this thesis to another author - subject this thesis to derogatory treatment which may prejudice the author’s reputation For further information contact the University’s Director of Copyright Services sydney.edu.au/copyright Influences on Research into the Origins of Life. Idan Ben-Barak Unit for the History and Philosophy of Science Faculty of Science The University of Sydney A thesis submitted to the University of Sydney as fulfilment of the requirements for the degree of Doctor of Philosophy 2014 Declaration I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person, nor material which to a substantial extent has been accepted for the award of any other degree or diploma of a University or other institute of higher learning. -
Jonathan BISSON
Jonathan BISSON Humans and Natural Products interaction Development of methods, software and databases for Natural Products research � bjonnh.net � linkedin.com/in/jonathanbisson � github.com/bjonnh �orcid.org/0000-0003-1640-9989 My main interest is the study of the interaction between Natural Products and Humans. My main objective is to make sense and make available the ideas, data and materials collected and created by Humans. To that end, I am developing an ontology that allows re- searchers and data analysts to use a common language to express ideas and concepts. The other aspect of my work is more traditional and consists in the discovery of new antibiotics against Tuberculosis and ESKAPE pathogens using mass-spectrometry and advanced data-analysis. � EDUCATION 2012 PhD Biology-Chemistry Interface, UNIVERSITY OF BORDEAUX, France 2009 First class honours, cum laude. Jury: Dr. Françoise Guéritte, Pr. Alain Berthod, Pr. Marcel Hibert, Pr. Philippe Jeandet, Patrice André, Pr. Jean-Michel Mérillon Director: Dr. Pierre Waffo-Téguo CPC NMR MS PYTHON LATEX PHYTOCHEMISTRY 2009 Master’s and Postgraduate’s Chemistry-Biology-Physics Interface, UNIVERSITY OF BORDEAUX, France 2004 Ranked 1st. NMR MS PHYTOCHEMISTRY BIOCHEMISTRY 2004 Associate Degree in industrial electrical engineering, LYCÉE GUSTAVE EIFFEL, Bordeaux, France 2003 Honorable mention. AUTOMATISM ELECTRICAL ENGINEERING � RESEARCH EXPERIENCE Today Visiting Research Assistant Professor, UNIVERSITY OF ILLINOIS AT CHICAGO, U.S.A. 2018 Digital Pharmacognosy, development of computational -
Grid Workflow Workshop 2011
Grid Workflow Workshop 2011 GWW 2011 MoSGrid: Progress of Workflow driven Chemical Simulations Georg Birkenheuer1∗, Dirk Blunk2, Sebastian Breuers2, Andre´ Brinkmann1, Gregor Fels3, Sandra Gesing4, Richard Grunzke5, Sonja Herres-Pawlis6, Oliver Kohlbacher4, Jens Kruger¨ 3, Ulrich Lang7, Lars Packschies7, Ralph Muller-Pfefferkorn¨ 5, Patrick Schafer¨ 8, Johannes Schuster1, Thomas Steinke8, Klaus-Dieter Warzecha7, and Martin Wewior7 1Paderborn Center for Parallel Computing, Universitat¨ Paderborn. 2Department fur¨ Chemie, Universitat¨ zu Koln.¨ 3Department Chemie, Universitat¨ Paderborn. 4Zentrum fur¨ Bioinformatik, Eberhard-Karls-Universitat¨ Tubingen.¨ 5Zentrum fur¨ Informationsdienste und Hochleistungsrechnen, Technische Universitat¨ Dresden. 6Fakultat¨ Chemie, Technische Universitat¨ Dortmund. 7Regionales Rechenzentrum, Universitat¨ zu Koln.¨ 8Konrad-Zuse-Institut fur¨ Informationstechnik Berlin. ABSTRACT Parallel to the extension of WS-PGRADE and gUSE for generic Motivation: Web-based access to computational chemistry grid workflows, MoSGrid started to implement intuitive portlets for the resources has proven to be a viable approach to simplify the use orchestration of specific workflows. The workflow application for of simulation codes. The introduction of recipes allows to reuse Molecular Dynamics is described in Section 3, followed by the already developed chemical workflows. By this means, workflows workflow application for Quantum Mechanics in Section 4. Section for recurring basic compute jobs can be provided for daily services. 5 covers the distributed data management for the workflow systems. Nevertheless, the same platform has to be open for active workflow development by experienced users. This paper provides an overview of recent developments of the MoSGrid project on providing tools and instruments for building workflow recipes. 2 THE WORKFLOW-ENABLED GRID PORTAL IN Contact: [email protected] MOSGRID The MoSGrid portal is developed on top of WS-PGRADE [3, 4], a workflow-enabled grid portal. -
Bioengineering an Open Access Journal by MDPI TRACKED for CITESCORE IMPACT 6.1 Bioengineering FACTOR SCOPUS an Open Access Journal by MDPI
TRACKED FOR CITESCORE IMPACT 6.1 FACTOR SCOPUS bioengineering an Open Access Journal by MDPI TRACKED FOR CITESCORE IMPACT 6.1 bioengineering FACTOR SCOPUS an Open Access Journal by MDPI Editor-in-Chief Message from the Editor-in-Chief Prof. Dr. Anthony Guiseppi-Elie You are invited to contribute a research article or a comprehensive review for consideration and publication in Bioengineering (ISSN 2306-5354). Bioengineering is published in open access format – research articles, reviews and other contents are released on the Internet immediately after acceptance. The scientific community and the general public have unlimited and free access to the content as soon as it is published. Bioengineering provides an advanced forum for the science and technology of bioengineering. We would be pleased to welcome you as one of our authors. Author Benefits Open Access Unlimited and free access for readers No Copyright Constraints Retain copyright of your work and free use of your article Thorough Peer-Review Fast Manuscript Handling Time A first decision provided to authors approximately 18.8 days after submission; acceptance to publication is undertaken in 3.8 days (median values for papers published in this journal in the first half of 2021) Coverage by Leading Indexing Services Indexed in Biological Abstracts and BIOSIS Previews (Web of Science), INSPEC (IET), PubMed(NLM) and Scopus No Space Constraints, No Extra Space or Color Charges No restriction on the length of the papers, number of figures or colors Discounts on Article Processing Charges (APC) If you belong to an institute that participates with the MDPI Institutional Open Access Program Aims and Scope Bioengineering (ISSN 2306-5354) publishes original research papers, comprehensive reviews, communications and case reports. -
2018 Journal Citation Reports Journals in the 2018 Release of JCR 2 Journals in the 2018 Release of JCR
2018 Journal Citation Reports Journals in the 2018 release of JCR 2 Journals in the 2018 release of JCR Abbreviated Title Full Title Country/Region SCIE SSCI 2D MATER 2D MATERIALS England ✓ 3 BIOTECH 3 BIOTECH Germany ✓ 3D PRINT ADDIT MANUF 3D PRINTING AND ADDITIVE MANUFACTURING United States ✓ 4OR-A QUARTERLY JOURNAL OF 4OR-Q J OPER RES OPERATIONS RESEARCH Germany ✓ AAPG BULL AAPG BULLETIN United States ✓ AAPS J AAPS JOURNAL United States ✓ AAPS PHARMSCITECH AAPS PHARMSCITECH United States ✓ AATCC J RES AATCC JOURNAL OF RESEARCH United States ✓ AATCC REV AATCC REVIEW United States ✓ ABACUS-A JOURNAL OF ACCOUNTING ABACUS FINANCE AND BUSINESS STUDIES Australia ✓ ABDOM IMAGING ABDOMINAL IMAGING United States ✓ ABDOM RADIOL ABDOMINAL RADIOLOGY United States ✓ ABHANDLUNGEN AUS DEM MATHEMATISCHEN ABH MATH SEM HAMBURG SEMINAR DER UNIVERSITAT HAMBURG Germany ✓ ACADEMIA-REVISTA LATINOAMERICANA ACAD-REV LATINOAM AD DE ADMINISTRACION Colombia ✓ ACAD EMERG MED ACADEMIC EMERGENCY MEDICINE United States ✓ ACAD MED ACADEMIC MEDICINE United States ✓ ACAD PEDIATR ACADEMIC PEDIATRICS United States ✓ ACAD PSYCHIATR ACADEMIC PSYCHIATRY United States ✓ ACAD RADIOL ACADEMIC RADIOLOGY United States ✓ ACAD MANAG ANN ACADEMY OF MANAGEMENT ANNALS United States ✓ ACAD MANAGE J ACADEMY OF MANAGEMENT JOURNAL United States ✓ ACAD MANAG LEARN EDU ACADEMY OF MANAGEMENT LEARNING & EDUCATION United States ✓ ACAD MANAGE PERSPECT ACADEMY OF MANAGEMENT PERSPECTIVES United States ✓ ACAD MANAGE REV ACADEMY OF MANAGEMENT REVIEW United States ✓ ACAROLOGIA ACAROLOGIA France ✓ -
Daftar E-Journal International Institut Teknologi Sumatera
DAFTAR E-JOURNAL INTERNATIONAL INSTITUT TEKNOLOGI SUMATERA PROGRAM STUDI : Teknik Kimia SUBJEK : Chemical Engineering Publisher: 1. Taylor and Francis 2. ScienceDirect 3. Springer Nature No Judul e-ISSN p-ISSN Link Penerbit Publikasi Anotasi Indexed/Abstracted in Chemical Engineering 1563-5201 0098-6445 https://e- Taylor and 12 issue(-s) Chemical Engineering Communications Abstracted/indexed in: CSA Communications resources.perpusnas.g Francis per annual provides a forum for the publication of Technology Research Database; o.id:2200/toc/gcec20/c manuscripts reporting on results of both Current Contents/Engineering, urrent basic and applied research in all areas of Computing, & Technology; chemical engineering. The journal's Engineering Index Monthly; Index audience includes researchers and Copernicus; and Science Citation practitioners in academia, industry, and Index. 1 government. Indian Chemical Engineer 0975-007X 0019-4506 https://e- Taylor and 4 issue(-s) Indian Chemical Engineer (ICE) is an Indian Chemical Engineer is resources.perpusnas.g Francis per annual international forum for the presentation of abstracted and indexed in: Scopus; o.id:2200/toc/tice20/cu original research, interpretative reviews and EBSCOhost; Electronics and rrent discussion on new developments in all areas Communications Abstracts; of chemical engineering and allied fields. It Information Express; IngentaConnect; contains papers describing novel theory and International Aerospace Abstracts; practical applications as well as reports of National Council for Cement and experimental work – carefully executed and Building Materials; OCLC ArticleFirst; soundly interpreted. It contains impartial, Process and Chemical Engineering; 2 generic papers or an overview of a Solid State and Superconductivity technology – intended to provide guidance Abstracts; Theoretical Chemical to practicing chemical engineers.