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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： Data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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Exploring nutritional supplement use for countering respiratory tract infections through an X (formerly Twitter)-based survey

Current Research in Biotechnology

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Current Research in Biotechnology 2025年 9卷

作者： Singla, Rajeev K. Mondal, Himel Singla, Shailja De, Ronita Behzad, Sahar Găman, Mihnea-Alexandru Sai Chandragiri, Siva Cenanovic, Merisa Patra, Jayanta Kumar Depew, Jennifer R. Boyina, Hemanth Kumar Maigoro, Abdulkadir Yusif Lee, Soojin Atrooz, Omar M. Das, Gitishree Schultz, Fabien Abdallah, Emad Mohamed Chopra, Hitesh Ahmad, Jamil Gautam, Rupesh K. Patnaik, Sourav S. Goh, Bey Hing Babiaka, Smith B. Vats, Sharad Okoh, Michael P. Ahmed, Atallah F. Dubey, Ankit Kumar Lordan, Ronan Subramani, Parasuraman Aiya Singh, Amit Kumar Alvarez-Suarez, José M. Chellappan, Dinesh Kumar Paswan, Shravan Kumar Semwal, Prabhakar Khan, Johra Sheshe, Sadeeq Sethiya, Neeraj Kumar Karpiński, Tomasz M. Riaz, Muhammad Emam-Djomeh, Zahra Gupta, Girish Kumar Madaan, Reecha Kumar, Suresh Choudhary, Neeraj Parisi, Salvatore Willschke, Harald Pirgozliev, Vasil Rayan, Rehab A. Ritschl, Valentin Mondal, Shaikat Zengin, Gokhan Verma, Pritt Kapoor, Bhupinder Gulati, Monica Balla, Gareeballah Osman Adam Le, Dan Khoa Pittalà, Valeria El-Demerdash, Amr Khalid, Garba M. Simal-Gandara, Jesus Alzahrani, Qushmua E. Russo, Gian Luigi Kharat, Kiran R. Bishayee, Anupam Wang, Dongdong Orhan, Ilkay Erdogan Ullah, Hammad Heinrich, Michael Baral, Bikash Tzvetkov, Nikolay T. Yeung, Andy Wai Kan Dias-Ferreira, João M.L. Olea, Scarlett Perez Mohanta, Yugal Kishore Kureshi, Azazahemad A. Supuran, Claudiu T. Rani, Neeraj Gundamaraju, Rohit Mulholland, Eoghan Joseph Lonardo, Sara Di Dinkova-Kostova, Albena T. González-Burgos, Elena Hritcu, Lucian Badhe, Pravin Singh, Abhilasha Al-Rimawi, Fuad Sureda, Antoni Abiri, Rambod Braidy, Nady Kapral, Lorenz Abdullahi, A.N. Medina, Christhian Delfino Villanueva Sheridan, Helen Lucarini, Massimo Durazzo, Alessandra Giampieri, Francesca Barreca, Davide Maria, Witkowska Anna Andrade, José Carlos Fimognari, Carmela Akram, Faizan Tikhonov, Aleksei Battino, Maurizio Oladipupo, Akolade R. Emerald, Mila Efferth, Thomas Amrani, Said Echeverría, Javier Maria Louka, Anna Tripathi, Surya Kant Fiebich, Bernd L. Es-Safi, Nour Eddine Khan Department of Critical Care Medicine and Institutes for Systems Genetics Frontiers Science Center for Disease-related Molecular Network West China Hospital Sichuan University Chengdu China Department of Physiology All India Institute of Medical Sciences Jharkhand Deoghar India iGlobal Research and Publishing Foundation New Delhi India Evidence-based Phytotherapy and Complementary Medicine Research Center Alborz University of Medical Sciences Karaj Iran Department of Hematology Center for Clinical and Basic Research (CCBR Clinic) Bucharest Romania Department of Cellular and Molecular Pathology Stefan S. Nicolau Institute of Virology Romanian Academy Bucharest Romania Department of Pathology University of Oklahoma Health Sciences Center Oklahoma City OK United States Sarajevo Bosnia and Herzegovina Research Institute of Integrative Life Sciences Dongguk University-Seoul Goyang-Si South Korea United States University Institute of Pharma Sciences Chandigarh University Punjab Mohali 140413 India Department of Microbiology and Molecular Biology College of Bioscience and Biotechnology Chungnam National University Daejeon 34134 South Korea Department of Biological Sciences Mutah University Jordan Ethnopharmacology & Zoopharmacognosy Research Group Department of Agriculture and Food Sciences Neubrandenburg University of Applied Sciences Germany Department of Biology College of Science Qassim University Buraydah 51452 Saudi Arabia Department of Biosciences Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Tamil Nadu Chennai 602105 India Department of Human Nutrition The University of Agriculture Peshawar Khyber Pakhtunkhwa 25120 Pakistan Department of Pharmacology Indore Institute of Pharmacy IIST Campus Rau (M.P.) Indore 453331 India The University of Texas Southwestern Medical Center Dallas TX United States Sunway Biofunctional Molecules Discovery Centre (SBMDC) School of Medical and Life Sciences Sunway University S

Background: Respiratory tract infections are a common health issue, driving interest in preventive strategies like nutritional supplements, while evidence on their usage and effectiveness remains limited. In this context, social media platforms, particularly X (formerly Twitter), provide a unique opportunity to gather large-scale public health-related data. Objectives: In this study, we aimed to survey participants’ uses and opinions on nutritional supplements in prevention or treatment of respiratory tract infections, by using X. Methods: A survey was conducted between 1st and 15th December 2022. A single open-ended question “Which are the best dietary supplements to counteract respiratory infections?“ was asked. One week after the start of the survey, a poll was posted to get more relevant information and boost the survey's reach. Total endorsements were calculated for each tweet posted as the total sum of replies, retweets, and likes. Results: The open-ended question received a total of 118 retweets, 39 quotes, and 371 likes, while the poll received 56 retweets, 13 quotes, and 67 likes. A total of 495 replies, 2,251 retweets, 5,118 likes, and 148 quotes were received for the question and its related tweets. Vitamin D (1,607 endorsements), zinc (1,347 endorsements), vitamin C (803 endorsements), magnesium (694 endorsements), and honey (661 endorsements) were the nutritional supplements that received most endorsements. Conclusion: Various foods, drinks, and natural ingredients have been suggested as potentially helpful for counteracting respiratory infections. Approximately half of respondents indicated using such supplements for themselves. The result of this study supports the idea that the X platform can be used as an effective survey tool to study global health-related behaviours and trends. © 2025 The Authors

关键词： Bacteria COVID-19 Nutritional supplements Phytomedicine Respiratory tract infections X (formerly Twitter)

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Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2024年第10期21卷 1959页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

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Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age

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Nature ecology & evolution 2025年 2025 May 22页

作者： Stephen Pringle Martin Dallimer Mark A Goddard Léni K Le Goff Emma Hart Simon J Langdale Jessica C Fisher Sara-Adela Abad Marc Ancrenaz Fabio Angeoletto Fernando Auat Cheein Gail E Austen Joseph J Bailey Katherine C R Baldock Lindsay F Banin Cristina Banks-Leite Aliyu S Barau Reshu Bashyal Adam J Bates Jake E Bicknell Jon Bielby Petra Bosilj Emma R Bush Simon J Butler Dan Carpenter Christopher F Clements Antoine Cully Kendi F Davies Nicolas J Deere Michael Dodd Rosie Drinkwater Don A Driscoll Guillaume Dutilleux Mads Dyrmann David P Edwards Mohammad S Farhadinia Aisyah Faruk Richard Field Robert J Fletcher Chris W Foster Richard Fox Richard M Francksen Aldina M A Franco Alison M Gainsbury Charlie J Gardner Ioanna Giorgi Richard A Griffiths Salua Hamaza Marc Hanheide Matt W Hayward Marcus Hedblom Thorunn Helgason Sui P Heon Kevin A Hughes Edmund R Hunt Daniel J Ingram George Jackson-Mills Kelly Jowett Timothy H Keitt Laura N Kloepper Stephanie Kramer-Schadt Jim Labisko Frédéric Labrosse Jenna Lawson Nicolas Lecomte Ricardo F de Lima Nick A Littlewood Harry H Marshall Giovanni L Masala Lindsay C Maskell Eleni Matechou Barbara Mazzolai Alistair McConnell Brett A Melbourne Aslan Miriyev Eric Djomo Nana Alessandro Ossola Sarah Papworth Catherine L Parr Ana Payo-Payo Gad Perry Nathalie Pettorelli Rajeev Pillay Simon G Potts Miranda T Prendergast-Miller Lan Qie Persie Rolley-Parnell Stephen J Rossiter Marcus Rowcliffe Heather Rumble Jon P Sadler Christopher J Sandom Asiem Sanyal Franziska Schrodt Sarab S Sethi Adi Shabrani Robert Siddall Simón C Smith Robbert P H Snep Carl D Soulsbury Margaret C Stanley Philip A Stephens P J Stephenson Matthew J Struebig Matthew Studley Martin Svátek Gilbert Tang Nicholas K Taylor Kate D L Umbers Robert J Ward Patrick J C White Mark J Whittingham Serge Wich Christopher D Williams Ibrahim B Yakubu Natalie Yoh Syed A R Zaidi Anna Zmarz Joeri A Zwerts Zoe G Davies Durrell Institute of Conservation and Ecology (DICE) School of Natural Sciences University of Kent Canterbury UK. s.pringle@kent.ac.uk. Centre for Environmental Policy Imperial College London London UK. Department of Geography and Environmental Sciences Northumbria University Newcastle upon Tyne UK. School of Computing Engineering and the Built Environment Edinburgh Napier University Edinburgh UK. Synthotech Ltd Milner Court Hornbeam Square Harrogate UK. Durrell Institute of Conservation and Ecology (DICE) School of Natural Sciences University of Kent Canterbury UK. Mechanical Engineering Department University College London London UK. HUTAN SWD Kota Kinabalu Malaysia. Programa de Pós-Graduação em Gestão e Tecnologia Ambiental da Universidade Federal de Rondonópolis Rondonópolis Brasil. Department of Engineering Harper Adams University Newport UK. Applied Ecology Research Group School of Life Sciences Anglia Ruskin University Cambridge UK. Centre for Ecology and Hydrology Penicuik UK. Department of Life Sciences Imperial College London Silwood Park Campus Ascot UK. Department of Urban and Regional Planning Faculty of Earth and Environmental Sciences Bayero University Kano Nigeria. Greenhood Nepal Kathmandu Nepal. Animal Rural & Environmental Sciences Nottingham Trent University Nottinghamshire UK. School of Biological and Environmental Sciences Liverpool John Moores University Liverpool UK. Lincoln Centre for Autonomous Systems University of Lincoln Lincoln UK. Royal Botanic Garden Edinburgh Edinburgh UK. School of Biological Sciences University of East Anglia Norwich Research Park Norwich UK. Digital Ecology Limited Bristol UK. School of Biological Sciences University of Bristol Bristol UK. Department of Computing Imperial College London London UK. Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA. Faculty of Science Technology Engineering and Mathematics (STEM) The Open University Walton Hall Milt

With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more 'difficult' taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.

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Author Correction: Why rankings of biomedical image analysis competitions should be interpreted with care

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Nature communications 2019年第1期10卷 588页

作者： Lena Maier-Hein Matthias Eisenmann Annika Reinke Sinan Onogur Marko Stankovic Patrick Scholz Tal Arbel Hrvoje Bogunovic Andrew P Bradley Aaron Carass Carolin Feldmann Alejandro F Frangi Peter M Full Bram van Ginneken Allan Hanbury Katrin Honauer Michal Kozubek Bennett A Landman Keno März Oskar Maier Klaus Maier-Hein Bjoern H Menze Henning Müller Peter F Neher Wiro Niessen Nasir Rajpoot Gregory C Sharp Korsuk Sirinukunwattana Stefanie Speidel Christian Stock Danail Stoyanov Abdel Aziz Taha Fons van der Sommen Ching-Wei Wang Marc-André Weber Guoyan Zheng Pierre Jannin Annette Kopp-Schneider Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. l.maier-hein@dkfz.de. Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Centre for Intelligent Machines McGill University Montreal QC H3A0G4 Canada. Christian Doppler Laboratory for Ophthalmic Image Analysis Department of Ophthalmology Medical University Vienna 1090 Vienna Austria. Science and Engineering Faculty Queensland University of Technology Brisbane QLD 4001 Australia. Department of Electrical and Computer Engineering Department of Computer Science Johns Hopkins University Baltimore MD 21218 USA. CISTIB - Center for Computational Imaging & Simulation Technologies in Biomedicine The University of Leeds Leeds Yorkshire LS2 9JT UK. Department of Radiology and Nuclear Medicine Medical Image Analysis Radboud University Center 6525 GA Nijmegen The Netherlands. Institute of Information Systems Engineering TU Wien 1040 Vienna Austria. Complexity Science Hub Vienna 1080 Vienna Austria. Heidelberg Collaboratory for Image Processing (HCI Heidelberg University 69120 Heidelberg Germany. Centre for Biomedical Image Analysis Masaryk University 60200 Brno Czech Republic. Electrical Engineering Vanderbilt University Nashville TN 37235-1679 USA. Institute of Medical Informatics Universität zu Lübeck 23562 Lübeck Germany. Division of Medical Image Computing (MIC) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Institute for Advanced Studies Department of Informatics Technical University of Munich 80333 Munich Germany. Information System Institute HES-SO Sierre 3960 Switzerland. Departments of Radiology Nuclear Medicine and Medical Informatics Erasmus MC 3015 GD Rotterdam The Netherlands. Department of Computer Science University of Warwick Coventry CV4 7AL UK. Department of Radiation Oncology Massachusetts General Hospital Boston MA

In the original version of this Article the values in the rightmost column of Table 1 were inadvertently shifted relative to the other columns. This has now been corrected in the PDF and HTML versions of the Article.

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Sustainable computational science: The Rescience initiative

arXiv

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arXiv 2017年

作者： Rougier, Nicolas P. Hinsen, Konrad Alexandre, Frédéric Arildsen, Thomas Barba, Lorena Benureau, Fabien C.Y. Titus Brown, C. de Buyl, Pierre Caglayan, Ozan Davison, Andrew P. Delsuc, Marc André Detorakis, Georgios Diem, Alexandra K. Drix, Damien Enel, Pierre Girard, Benoît Guest, Olivia Hall, Matt G. Henriques, Rafael Neto Hinaut, Xavier Jaron, Kamil S. Khamassi, Mehdi Klein, Almar Manninen, Tiina Marchesi, Pietro McGlinn, Dan Metzner, Christoph Petchey, Owen L. Plesser, Hans Ekkehard Poisot, Timothée Ram, Karthik Ram, Yoav Roesch, Etienne Rossant, Cyrille Rostami, Vahid Shifman, Aaron Stimberg, Marcel Stachelek, Joseph Stollmeier, Frank Vaggi, Federico Viejo, Guillaume Vitay, Julien Vostinar, Anya Yurchak, Roman Zito, Tiziano INRIA Bordeaux Sud-Ouest Talence France Institut des Maladies Neurodégénératives Université de Bordeaux CNRS UMR 5293 Bordeaux France LaBRI Université de Bordeaux Bordeaux INP CNRS UMR 5800 Talence France Centre de Biophysique Moléculaire CNRS UPR4301 Orléans France Synchrotron SOLEIL Division Expériences Gif sur Yvette France Department of Electronic Systems Technical Faculty of IT and Design Aalborg University Denmark Department of Mechanical and Aerospace Engineering George Washington University WashingtonDC United States Department of Population Health and Reproduction University of California Davis DavisCA United States Instituut voor Theoretische Fysica KU Leuven Belgium Le Mans France Unité de Neurosciences Information et Complexité CNRS FRE 3693 Gif sur Yvette France Institut de Génétique et de Biologie Moléculaire et Cellulaire INSERM U964 CNRS UMR 7104 Université de Strasbourg Illkirch France Department of Cognitive Sciences University of California Irvine United States Computational Engineering and Design Faculty of Engineering and the Environment University of Southampton United Kingdom Department of Computer Science Humboldt-Universität zu Berlin Friedman Brain Institute Icahn School of Medicine Mount SinaiNY United States Institut des Systèmes Intelligent et de Robotique Sorbonne Universités UPMC Univ Paris 06 CNRS Paris France Experimental Psychology University College London United Kingdom UCL Great Ormond St Institute of Child Health University College London London United Kingdom MRC Cognition and Brain Sciences Unit Cambridge United Kingdom Department of Ecology and Evolution University of Lausanne Lausanne Switzerland Independent scholar Enschede Netherlands BioMediTech Institute and Faculty of Biomedical Sciences and Engineering Tampere University of Technology Tampere Finland Swammerdam Institute for Life Sciences Center for Neuroscience Faculty of Science University of Amsterdam Amsterdam Netherlands Depart

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. Jonathan Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. Rescience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. Rescience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests. Copyright © 2017, The Authors. All rights reserved.

关键词： Open source software

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Computational science and Its Applications – ICCSA 2012 1

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丛书名： Lecture Notes in Computer science

1000年

作者： Beniamino Murgante Osvaldo Gervasi Sanjay Misra Nadia Nedjah Ana Maria A. C. Rocha David Taniar Bernady O. Apduhan

ISBN: (数字)9783642311253

ISBN: (纸本)9783642311246

The four-volume set LNCS 7333-7336 constitutes the refereed proceedings of the 12th International Conference on Computational science and Its Applications, ICCSA 2012, held in Salvador de Bahia, Brazil, in June 2012. The four volumes contain papers presented in the following workshops: 7333 - advances in high performance algorithms and applications (AHPAA); bioinspired computing and applications (BIOCA); computational geometry and applicatons (CGA); chemistry and materials sciences and technologies (CMST); cities, technologies and planning (CTP); 7334 - econometrics and multidimensional evaluation in the urban environment (EMEUE); geographical analysis, urban modeling, spatial statistics (Geo-An-Mod); 7335 - optimization techniques and applications (OTA); mobile communications (MC); mobile-computing, sensind and actuation for cyber physical systems (MSA4CPS); remote sensing (RS); 7336 - software engineering processes and applications (SEPA); software quality (SQ); security and privacy in computational sciences (SPCS); soft computing and data engineering (SCDE). The topics of the fully refereed papers are structured according to the four major conference themes: 7333 - computational methods, algorithms and scientific application; 7334 - geometric modelling, graphics and visualization; 7335 - information systems and technologies; 7336 - high performance computing and networks.

关键词： Computer Communication Networks Algorithm Analysis and Problem Complexity Software Engineering Simulation and Modeling Information systems Applications (incl. Internet) Data Mining and Knowledge Discovery

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Computational science and Its Applications – ICCSA 2012 1

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丛书名： Lecture Notes in Computer science

1000年

作者： Beniamino Murgante Osvaldo Gervasi Sanjay Misra Nadia Nedjah Ana Maria A. C. Rocha David Taniar Bernady O. Apduhan

ISBN: (数字)9783642310751

ISBN: (纸本)9783642310744

The four-volume set LNCS 7333-7336 constitutes the refereed proceedings of the 12th International Conference on Computational science and Its Applications, ICCSA 2012, held in Salvador de Bahia, Brazil, in June 2012.;The four volumes contain papers presented in the following workshops: 7333 - advances in high performance algorithms and applications (AHPAA); bioinspired computing and applications (BIOCA); computational geometry and applicatons (CGA); chemistry and materials sciences and technologies (CMST); cities, technologies and planning (CTP); 7334 - econometrics and multidimensional evaluation in the urban environment (EMEUE); geographical analysis, urban modeling, spatial statistics (Geo-An-Mod); 7335 - optimization techniques and applications (OTA); mobile communications (MC); mobile-computing, sensind and actuation for cyber physical systems (MSA4CPS); remote sensing (RS); 7336 - software engineering processes and applications (SEPA); software quality (SQ); security and privacy in computational sciences (SPCS); soft computing and data engineering (SCDE).;The topics of the fully refereed papers are structured according to the four major conference themes: 7333 - computational methods, algorithms and scientific application; 7334 - geometric modelling, graphics and visualization; 7335 - information systems and technologies; 7336 - high performance computing and networks.

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Computational science and Its Applications – ICCSA 2012 1

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丛书名： Lecture Notes in Computer science

1000年

作者： Beniamino Murgante Osvaldo Gervasi Sanjay Misra Nadia Nedjah Ana Maria A. C. Rocha David Taniar Bernady O. Apduhan

ISBN: (数字)9783642311284

ISBN: (纸本)9783642311277

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SOFSEM 2012: Theory and Practice of Computer science 1

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丛书名： Lecture Notes in Computer science

1000年

作者： Mária Bieliková Gerhard Friedrich Georg Gottlob Stefan Katzenbeisser György Turán

ISBN: (数字)9783642276606

ISBN: (纸本)9783642276590

This book constitutes the refereed proceedings of the 38th Conference on Current Trends in Theory and Practice of Computer science, SOFSEM 2012, held in Špindlerův Mlýn, Czech Republic, in January 2012. The 43 revised papers presented in this volume were carefully reviewed and selected from 121 submissions. The book also contains 11 invited talks, 10 of which are in full-paper length. The contributions are organized in topical sections named: foundations of computer science; software and Web engineering; cryptography, security, and verification; and artificial intelligence.

关键词： Algorithm Analysis and Problem Complexity Software Engineering Data Storage Representation Discrete Mathematics in Computer science Computer Communication Networks Database Management

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