Relevant bibliographies by topics / Scientific Notebook

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Scientific Notebook'

Author: Grafiati
Published: 4 June 2021
Last updated: 26 January 2023

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Journal articles on the topic "Scientific Notebook"

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Reich, Michael M., Thorin Tabor, Edwin Juarez, Alexander Wenzel, Ted Liefeld, Barbara Hill, David Eby, et al. "Abstract 1903: GenePattern Notebook: An integrative analytical environment for cancer research." Cancer Research 82, no. 12_Supplement (June 15, 2022): 1903. http://dx.doi.org/10.1158/1538-7445.am2022-1903.

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Abstract As the availability of genomic data and analysis tools from large-scale cancer initiatives continues to increase, with single-cell studies adding new dimensions to the potential scientific insights, the need has become more urgent for a software environment that supports the rapid pace of cancer data science. The electronic analysis notebook has recently emerged as a versatile tool for this purpose, allowing scientists to combine the scientific exposition with the code that runs the analysis, creating a single “research narrative” document. The Jupyter Notebook system has become the de facto standard notebook environment in data science and genomic analysis. However, the Jupyter environment requires familiarity with programming to run analyses, and even text must be formatted using a programming-style language.To extend notebook capabilities to researchers at all levels of programming expertise, we developed the GenePattern Notebook environment, which integrates Jupyter with the hundreds of genomic tools available through the GenePattern platform. This tool allows scientists to develop, share, collaborate on, and publish their notebooks, requiring only a web browser. Investigators can design their in-silico experiments, refine workflows, launch compute-intensive analyses on cloud-based and high-performance compute resources, and publish results that others can adopt to reproduce the original analyses and modify for their own work.GenePattern Notebook provides: (1) Access to a wide range of genomic analyses within a notebook. Hundreds of analyses are available, from machine learning techniques such as clustering, classification, and dimension reduction, to omic-specific methods for gene expression analysis, proteomics, flow cytometry, sequence variation analysis, pathway analysis, and others. (2) A library of featured genomic analysis notebooks, including templates for common analysis tasks as well as cancer-specific research scenarios and compute-intensive methods. Scientists can easily copy these notebooks, use them as is, or adapt them for their research purposes. To support the growing role of single-cell analysis, we have recently released single-cell RNA-seq preprocessing, cluster harmonization, pseudotime, and RNA velocity notebooks. (3) Notebook enhancements. A rich text editor allows scientists to format text as they would in a word processor. A user interface-building tool allows notebook developers to wrap code so it is displayed as a web form, with only the necessary inputs exposed. (4) Publication and collaborative editing. Authors can publish their notebooks, where they are then made available on the community section of the notebook workspace, where other scientists may copy, run, and edit their own version.The GenePattern Notebook environment is freely available at http://genepattern-notebook.org. Citation Format: Michael M. Reich, Thorin Tabor, Edwin Juarez, Alexander Wenzel, Ted Liefeld, Barbara Hill, David Eby, Forrest Kim, Helga Thorvaldsdóttir, Pablo Tamayo, Jill P. Mesirov. GenePattern Notebook: An integrative analytical environment for cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1903.
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Lewin, Jonathan, and MacKichan Software Inc. "What is Scientific Notebook?" College Mathematics Journal 33, no. 5 (November 2002): 426. http://dx.doi.org/10.2307/1559021.

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Migliorini Mendes, Reisila Simone, Juliana Nascimento Magno, Flávia Moreira Gomes, Fernanda de Jesus Costa, Gracielle Pereira Pimenta Bragança, Nina Castro Jorge, and Rosy Mary dos Santos Isaias. "Do we need plants to survive? Triggering interest in Plant Science." Research, Society and Development 12, no. 1 (January 9, 2023): e23712139614. http://dx.doi.org/10.33448/rsd-v12i1.39614.

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The concept of plant blindness deals with the human inability to perceive the plants around, although they are essential for the basis of life on Earth. Furthermore, the daily human coexistence with plants or with products derived from plants is indisputable. We look for strategies to reverse the perceptive capacity of plants in our daily lives, bringing the Scientia amabilis; to the foreground, focusing on Botany as a fundamental area of Biological Sciences. We proposed to undergraduate students of Biological Science the production of a botany notebook in which they record their daily experiences with plants and plant-derived products. The activity was carried out in four steps: (1) production of the text; (2) a conversation circle; (3) insertion of scientific botanical data in the notebooks; and (4) analysis of the notebook text contents. The relationships established by the students focused on the utilitarian perception. The scientific approaches followed mostly the logic of the textbooks, with emphasis on plant structures, followed by plant systematics and physiology. The analysis of the texts and the narrative of the students allows us to conclude that the production of the Botany Notebooks improved the students' perception the importance of plants for human survival and served as a trigger for interest in discussions of botanical the environmental balance and the maintenance of all levels of life on Earth.
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Pendley, Bradford D. "Keeping a Scientific Notebook: The Lego Exercise." Journal of Chemical Education 74, no. 9 (September 1997): 1065. http://dx.doi.org/10.1021/ed074p1065.1.

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Richardson, Michael L., and Behrang Amini. "Scientific Notebook Software: Applications for Academic Radiology." Current Problems in Diagnostic Radiology 47, no. 6 (November 2018): 368–77. http://dx.doi.org/10.1067/j.cpradiol.2017.09.005.

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Yakimchik, A. I. "Jupyter Notebook: a system for interactive scientific computing." Geofizicheskiy Zhurnal 41, no. 2 (April 17, 2019): 121. http://dx.doi.org/10.24028/gzh.0203-3100.v41i2.2019.164458.

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Goddard, Nigel H., Rory Macneil, and Jonathan Ritchie. "eCAT: Online electronic lab notebook for scientific research." Automated Experimentation 1, no. 1 (2009): 4. http://dx.doi.org/10.1186/1759-4499-1-4.

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Richardson, Michael L., and Behrang Amini. "Teaching Radiology Physics Interactively with Scientific Notebook Software." Academic Radiology 25, no. 6 (June 2018): 801–10. http://dx.doi.org/10.1016/j.acra.2017.11.024.

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HORSMAN, FRANK. "Ralph Johnson's notebook." Archives of Natural History 22, no. 2 (June 1995): 147–67. http://dx.doi.org/10.3366/anh.1995.22.2.147.

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A botanical notebook is identified as Ralph Johnson's (1629–1695) of Brignall in North Yorkshire. Johnson was a great friend of John Ray (1627–1705). The dates of the notebook are established as 1649–1672, the botanical notes having been made in 1671–1672. The notebook demonstrates that Ray put Johnson's interest in botany on a scientific basis, in line with Johnson's studies of birds and fishes. It also permits a personal insight into the impact of the first edition of Ray's Catalogus Plantarum Angliae (1670) on British botany. The notebook demonstrates Ray's personal influence on the botanical discovery of Upper Teesdale, one of our most important botanical areas. An attempt is made to rectify the situation whereby Johnson is totally overlooked, despite Ray's very high opinion of him as a naturalist.
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Wagemann, Julia, Federico Fierli, Simone Mantovani, Stephan Siemen, Bernhard Seeger, and Jörg Bendix. "Five Guiding Principles to Make Jupyter Notebooks Fit for Earth Observation Data Education." Remote Sensing 14, no. 14 (July 12, 2022): 3359. http://dx.doi.org/10.3390/rs14143359.

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There is a growing demand to train Earth Observation (EO) data users in how to access and use existing and upcoming data. A promising tool for data-related training is computational notebooks, which are interactive web applications that combine text, code and computational output. Here, we present the Learning Tool for Python (LTPy), which is a training course (based on Jupyter notebooks) on atmospheric composition data. LTPy consists of more than 70 notebooks and has taught over 1000 EO data users so far, whose feedback is overall positive. We adapted five guiding principles from different fields (mainly scientific computing and Jupyter notebook research) to make the Jupyter notebooks more educational and reusable. The Jupyter notebooks developed (i) follow the literate programming paradigm by a text/code ratio of 3, (ii) use instructional design elements to improve navigation and user experience, (iii) modularize functions to follow best practices for scientific computing, (iv) leverage the wider Jupyter ecosystem to make content accessible and (v) aim for being reproducible. We see two areas for future developments: first, to collect feedback and evaluate whether the instructional design elements proposed meet their objective; and second, to develop tools that automatize the implementation of best practices.
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Dissertations / Theses on the topic "Scientific Notebook"

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Zaki, Zulkifly Mohd. "A user-orientated electronic laboratory notebook for the retrieval of scientific provenance grounded in EUROCHAMP-2 community." Thesis, University of Leeds, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.581944.

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Data is particularly valuable to scientists when details of its provenance are known. The traditional means of capturing provenance of experimental work is a scientist's personal laboratory notebook. The process is often ad-hoc and its content unstructured, making it hard to share the underlying scientific thoughts with other scientists. A better alternative to this traditional method of capturing provenance is now possible by using Electronic Laboratory Notebooks (ELNs) [1]. This research is concerned with deploying a user-orientated Electronic Laboratory Notebook (uELN) system within a scientific community. The uELN system supported the capture and retrieval of simulation data describing the provenance of the modelling activities of scientists within that community. The research was grounded within the atmospheric chemistry community. The uELN system involved the automatic capture of data concerning the modelling process together with inline annotations added by the modeller explaining the reasoning for modelling decisions at each step of the process. A full realisation of the uELN system was built for the atmospheric chemistry community. An ontology (in OWL) was used to ensure the specific terminology of the community was used within the provenance data and also that it was used consistently. The architecture included a dynamic graphic interface that allows the modeller to view hislher modelling history. This was recorded as a set of nodes each pointing to the stored provenance data associated with a specific simulation run. In addition, there was an innovative mechanism that enabled the modeller to navigate through the various nodes. The navigation process supported comparisons between different nodes: a facility that users found particularly valuable. Two types of user-centred evaluations (i.e. formative and summative) were undertaken with members of the atmospheric chemistry community. In formative evaluation, the usability of uELN design was improved. In summative evaluation, a two-day workshop was conducted. This confirmed the value of the uELN to the modellers and it is now being introduced more widely across the modelling community.
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Kanza, Samantha. "What influence would a cloud based semantic laboratory notebook have on the digitisation and management of scientific research?" Thesis, University of Southampton, 2018. https://eprints.soton.ac.uk/421045/.

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Electronic laboratory notebooks (ELNs) have been studied by the chemistry research community over the last two decades as a step towards a paper-free laboratory; similar work has also taken place in other laboratory science domains. However, despite the many available ELN platforms, their uptake in both the academic and commercial worlds remains limited. This thesis describes an investigation into the current ELN landscape, and its relationship with the requirements of laboratory scientists. Market and literature research was conducted around available ELN offerings to characterise their commonly incorporated features. Previous studies of laboratory scientists examined note-taking and record-keeping behaviours in laboratory environments; to complement and extend this, a series of user studies were conducted as part of this thesis, drawing upon the techniques of user-centred design, ethnography, and collaboration with domain experts. These user studies, combined with the characterisation of existing ELN features, informed the requirements and design of a proposed ELN environment which aims to bridge the gap between scientists' current practice using paper lab notebooks, and the necessity of publishing their results electronically, at any stage of the experiment life cycle. The proposed ELN environment uses a three-layered approach: a notebook layer consisting of an existing cloud based notebook; a domain specific layer with the appropriate knowledge; and a semantic layer that tags and marks-up documents. A prototype of the semantic layer (Semanti-Cat) was created for this thesis, and evaluated with respect to the sociological techniques: Actor Network Theory and the Unied Theory of Acceptance and Use of Technology. This thesis concludes by considering the implications of this ELN environment on broader laboratory practice. The results of the user studies in this thesis have underscored laboratory scientists' attachment to paper lab notebooks; however, even though paper lab notebooks are currently unlikely to be replaced by a system of digitised experimental records, laboratory scientists are not opposed to using technology that facilitates high-level integration, management and organisation of their records. This thesis therefore identifies areas of improvement in current laboratory data management software.
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Reed, Melinda. "Science notebooks: improving students' conceptual understanding and scientific practices." Montana State University, 2012. http://etd.lib.montana.edu/etd/2012/reed/ReedM0812.pdf.

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The objective of this study was to determine if using science notebooks improved students' understandings of science content. Secondary considerations included whether or not science notebooks versus commercial worksheets impacted students' scientific practices and communication skills. This study contained two treatment phases. In the first phase, students used commercial textbooks and worksheets in an Earth Science Unit. During the second phase of the study student science notebooks were introduced and replaced the commercial worksheets during a Physical Science Unit. At the beginning and end of both phases of the study, a student pre and post-test were administered in each content area. Throughout both phases, a variety of formative assessments such as lab reports, concept maps, assessment probes, and other assignments were implemented and evaluated. As a result of this study, it was concluded that student science notebooks did improve students' conceptual understandings. Formative and summative assessments indicated use of science notebooks led to quantifiable growth in conceptual understandings, scientific practices, and communications skills.
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Marques, Bruno Monteiro. "Dendro Research Notebook: Interactive Scientific Visualizations for e-Science." Master's thesis, 2020. https://hdl.handle.net/10216/127085.

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Marques, Bruno Monteiro. "Dendro Research Notebook: Interactive Scientific Visualizations for e-Science." Dissertação, 2020. https://hdl.handle.net/10216/127085.

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Roberts, Nathan William. "Automation of Laboratory Activities Through Integration of an Electronic Laboratory Notebook (ELN) with a Scientific Data Management System (SDMS)." Thesis, 2006. http://hdl.handle.net/1805/593.

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Submitted to the faculty of the School of Informatics in partial fulfillment of the requirements for the degree Master of Science in Chemical Informatics (Laboratory Informatics Specialization), Indiana University, June 2006
Industry and academic laboratories have long resisted conversion to electronic laboratory notebooks (ELN) while at the same time integrating many other kinds of information systems, most notably laboratory information management systems (LIMS), chromatography data systems (CDS), and scientific data management systems (SDMS), within laboratory operations. Scientists in both academia and industry stand to gain important functionality unavailable with paper notebooks with the adoption of ELNs such as comprehensive searching of notebooks (keyword, result, and molecular structure/substructure searching, for example); distributed availability; and long term access to data. Currently, most laboratory information systems operate independently, requiring manual data entry by users into each individual system. This process creates data and information disparities as well as creating poor referential integrity within experimental metadata. Electronic laboratory notebooks would provide a logical point around which experiment details and observations could be centered electronically. Through an ELN, experimental documentation or metadata could be communicated automatically with a LIMS, SDMS, or CDS without analyst involvement. This “electronically connected” system would allow analysts to perform their responsibilities without the interruption of independent information systems thus increasing analyst productivity and reducing user entry errors into data management systems. The thesis project consisted of two phases: the first phase was the implementation of an ELN and the second phase was the development of a software developer kit (SDK) for LABTrack based on Web Services. In the first phase of the project the adoption of an ELN, was studied within a classroom laboratory (G823 Introduction to Cell Biology) over the course of one academic semester. In the second phase of the project an SDK for LABTrack was developed to allow the importation of information from custom developed applications into LABTrack. Finally, a web portal integrating LABTrack and NuGenesis was developed to demonstrate the capabilities of the LABTrack SDK and existing capabilities of the NuGenesis SDK.
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Books on the topic "Scientific Notebook"

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Anne, Bagby Susan, ed. Getting started with Scientific WorkPlace, Scientific Word, and Scientific Notebook: Version 3.5. Bainbridge Island, Wash: MacKichan Software Inc., 2000.

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1935-, Walker Carol L., ed. Doing calculus with Scientific Notebook. Las Cruces, N.M: TCI Software Research, 1997.

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Einführung in Scientific WorkPlace, Scientific Word, und Scientific Notebook: Version 4.0. Bainbridge Island, Wa: MacKichan Software Inc., 2001.

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1935-, Walker Carol L., ed. Doing mathematics with Scientific WorkPlace and Scientific Notebook: Users' guide to computing version 3.5. Bainbridge Island, WA: MacKichan Software, 2000.

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Jonathan, Lewin, ed. Exploring mathematics with scientific notebook. Singapore: Springer, 1998.

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Joseph, Gallant. Doing Physics with Scientific Notebook. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.

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Gallant, Joseph. Doing physics with Scientific Notebook: A problem solving approach. Hoboken, N.J: Wiley, 2012.

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Author, Walker Carol L., ed. Doing mathematics with Scientific WorkPlace® and Scientific Notebook®: Users' guide to computing, version 5. Poulsbo, Wash: MacKichan Software, Inc., 2003.

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Amici, Giovanni Battista. Opere edite =: Edited scientific papers. Napoli: Bibliopolis, 2006.

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Scientific Lab Notebook. Hayden Mcneil Pub, 2002.

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Book chapters on the topic "Scientific Notebook"

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de Mûelenaere, Gwendoline. "The Art of Learning: Illustrated Lecture Notebooks at the Old University of Louvain." In Scientific Visual Representations in History, 3–31. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-11317-8_1.

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Samuel, Sheeba, and Birgitta König-Ries. "Combining P-Plan and the REPRODUCE-ME Ontology to Achieve Semantic Enrichment of Scientific Experiments Using Interactive Notebooks." In Lecture Notes in Computer Science, 126–30. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-98192-5_24.

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"IPython and Jupyter Notebook." In Learning Scientific Programming with Python, 172–95. Cambridge University Press, 2020. http://dx.doi.org/10.1017/9781108778039.006.

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"Topics in Classical Physics." In Doing Physics with Scientific Notebook, 397–434. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.app1.

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"Topics in Modern Physics." In Doing Physics with Scientific Notebook, 435–89. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.app2.

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"Introduction to SNB." In Doing Physics with Scientific Notebook, 1–82. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.ch1.

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"Fluids." In Doing Physics with Scientific Notebook, 309–34. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.ch10.

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"Temperature and Heat." In Doing Physics with Scientific Notebook, 335–57. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.ch11.

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"Special Relativity." In Doing Physics with Scientific Notebook, 359–96. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.ch12.

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"One-Dimensional Kinematics." In Doing Physics with Scientific Notebook, 83–104. The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK: John Wiley & Sons, Ltd, 2012. http://dx.doi.org/10.1002/9781119941576.ch2.

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Conference papers on the topic "Scientific Notebook"

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Yakimchik, A. I., and S. O. Shabatura. "About Scientific Computing within Python and Jupyter Notebook." In 18th International Conference on Geoinformatics - Theoretical and Applied Aspects. European Association of Geoscientists & Engineers, 2019. http://dx.doi.org/10.3997/2214-4609.201902091.

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Vostokin, S., S. Popov, and O. Sukhoroslov. "EXPERIENCE IN ORGANIZING FLEXIBLE ACCESS TO REMOTE COMPUTING RESOURCES FROM JUPYTERLAB ENVIRONMENT USING TECHNOLOGIES OF EVEREST AND TEMPLET PROJECTS." In 9th International Conference "Distributed Computing and Grid Technologies in Science and Education". Crossref, 2021. http://dx.doi.org/10.54546/mlit.2021.94.77.001.

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The paper describes the experience of building distributed web applications based on the interactivecomputing technologies of the Jupyter project. The new architecture of such applications is proposed,considering the possibility of deploying a Jupyter notebook server separately from computingresources, and the possibility to interact with several computing resources simultaneously. Thesefeatures are implemented using the Everest platform for resource integration and the Templet SDK foraccessing the platform from Jupyter notebooks. Two examples of computing and data processingapplications built on this architecture are discussed. The proposed solutions are designed to automateresource-intensive computing activities in scientific and research projects.
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Matiakina, Ellina Nikolaevna. "VISUAL STYLES OF COMPUTER GAMES." In International Scientific and Practical Conference for Students, chair Marina Mikhailovna Novikova. TSNS Interaktiv Plus, 2019. http://dx.doi.org/10.21661/r-497135.

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The article is devoted to the Visual styles of computer games, their links with the traditions of classic graphics and animations, a comparative analysis is carried out on a sample of games "GRIS", "Child of Light", and "Neverending Nightmares", "Cat Notebook", "The Whispered World", "Don't Starve," "Paper Moon", "Okami" and other
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Ionascu, Alexandru, and Sebastian-Aurelian Stefaniga. "DS Lab Notebook: A new tool for data science applications." In 2020 22nd International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC). IEEE, 2020. http://dx.doi.org/10.1109/synasc51798.2020.00056.

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Oleksik, Gerard, Natasa Milic-Frayling, and Rachel Jones. "Study of electronic lab notebook design and practices that emerged in a collaborative scientific environment." In CSCW'14: Computer Supported Cooperative Work. New York, NY, USA: ACM, 2014. http://dx.doi.org/10.1145/2531602.2531709.

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Slominski, Aleksander. "Flexible Creation and Adaptive Execution of Scientific Workflows in Cloud and Grid Environments by Using Web 2.0-Based Electronic Lab Notebook Metaphor." In 2010 IEEE Congress on Services (SERVICES). IEEE, 2010. http://dx.doi.org/10.1109/services.2010.28.

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Atkins, Leslie J., and Irene Y. Salter. "Using scientists' notebooks to foster authentic scientific practices." In 2012 PHYSICS EDUCATION RESEARCH CONFERENCE. AIP, 2013. http://dx.doi.org/10.1063/1.4789649.

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Savira, Pambayun, Thomas Marrinan, and Michael E. Papka. "Writing, Running, and Analyzing Large-scale Scientific Simulations with Jupyter Notebooks." In 2021 IEEE 11th Symposium on Large Data Analysis and Visualization (LDAV). IEEE, 2021. http://dx.doi.org/10.1109/ldav53230.2021.00020.

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Gede, Gilbert, Dale L. Peterson, Angadh S. Nanjangud, Jason K. Moore, and Mont Hubbard. "Constrained Multibody Dynamics With Python: From Symbolic Equation Generation to Publication." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-13470.

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Symbolic equations of motion (EOMs) for multibody systems are desirable for simulation, stability analyses, control system design, and parameter studies. Despite this, the majority of engineering software designed to analyze multibody systems are numeric in nature (or present a purely numeric user interface). To our knowledge, none of the existing software packages are 1) fully symbolic, 2) open source, and 3) implemented in a popular, general, purpose high level programming language. In response, we extended SymPy (an existing computer algebra system implemented in Python) with functionality for derivation of symbolic EOMs for constrained multibody systems with many degrees of freedom. We present the design and implementation of the software and cover the basic usage and workflow for solving and analyzing problems. The intended audience is the academic research community, graduate and advanced undergraduate students, and those in industry analyzing multibody systems. We demonstrate the software by deriving the EOMs of a N-link pendulum, show its capabilities for LATEX output, and how it integrates with other Python scientific libraries — allowing for numerical simulation, publication quality plotting, animation, and online notebooks designed for sharing results. This software fills a unique role in dynamics and is attractive to academics and industry because of its BSD open source license which permits open source or commercial use of the code.
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