Relevant bibliographies by topics / Biology Research Computer programs

Academic literature on the topic 'Biology Research Computer programs'

Author: Grafiati
Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Biology Research Computer programs"

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Ofria, Charles, and Claus O. Wilke. "Avida: A Software Platform for Research in Computational Evolutionary Biology." Artificial Life 10, no. 2 (March 2004): 191–229. http://dx.doi.org/10.1162/106454604773563612.

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Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.
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Caudill, Lester, April Hill, Kathy Hoke, and Ovidiu Lipan. "Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines." CBE—Life Sciences Education 9, no. 3 (September 2010): 212–16. http://dx.doi.org/10.1187/cbe.10-03-0020.

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Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.
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Reeves, Aaron. "MicroMeasure: A new computer program for the collection and analysis of cytogenetic data." Genome 44, no. 3 (June 1, 2001): 439–43. http://dx.doi.org/10.1139/g01-037.

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The ability to identify individual chromosomes in cytological preparations is an essential component of many investigations. While several computer software applications have been used to facilitate such quantitative karyotype analysis, most of these programs are limited by design for specific types of analyses, or can be used only with specific hardware configurations. MicroMeasure is a new image analysis application that may be used to collect data for a wide variety of chromosomal parameters from electronically captured or scanned images. Unlike similar applications, MicroMeasure may be individually configured by the end user to suit a wide variety of research needs. This program can be used with most common personal computers, and requires no unusual or specific hardware. MicroMeasure is made available to the research community without cost by the Department of Biology at Colorado State University via the World Wide Web at http://www.biology.colostate.edu/MicroMeasure.Key words: MicroMeasure, computer program, chromosome measurement, cytogenetics.
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Krilowicz, Beverly, Wendie Johnston, Sandra B. Sharp, Nancy Warter-Perez, and Jamil Momand. "A Summer Program Designed to Educate College Students for Careers in Bioinformatics." CBE—Life Sciences Education 6, no. 1 (March 2007): 74–83. http://dx.doi.org/10.1187/cbe.06-03-0150.

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A summer program was created for undergraduates and graduate students that teaches bioinformatics concepts, offers skills in professional development, and provides research opportunities in academic and industrial institutions. We estimate that 34 of 38 graduates (89%) are in a career trajectory that will use bioinformatics. Evidence from open-ended research mentor and student survey responses, student exit interview responses, and research mentor exit interview/survey responses identified skills and knowledge from the fields of computer science, biology, and mathematics that are critical for students considering bioinformatics research. Programming knowledge and general computer skills were essential to success on bioinformatics research projects. General mathematics skills obtained through current undergraduate natural sciences programs were adequate for the research projects, although knowledge of probability and statistics should be strengthened. Biology knowledge obtained through the didactic phase of the program and prior undergraduate education was adequate, but advanced or specific knowledge could help students progress on research projects. The curriculum and assessment instruments developed for this program are available for adoption by other bioinformatics programs at http://www.calstatela.edu/SoCalBSI .
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Oxford, Julia Thom, Ken A. Cornell, Jared J. Romero, Diane B. Smith, Tracy L. Yarnell, Rhiannon M. Wood, Cheryl L. Jorcyk, et al. "Center of Biomedical Research Excellence in Matrix Biology: Building Research Infrastructure, Supporting Young Researchers, and Fostering Collaboration." International Journal of Molecular Sciences 21, no. 6 (March 20, 2020): 2141. http://dx.doi.org/10.3390/ijms21062141.

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The Center of Biomedical Research Excellence in Matrix Biology strives to improve our understanding of extracellular matrix at molecular, cellular, tissue, and organismal levels to generate new knowledge about pathophysiology, normal development, and regenerative medicine. The primary goals of the Center are to i) support junior investigators, ii) enhance the productivity of established scientists, iii) facilitate collaboration between both junior and established researchers, and iv) build biomedical research infrastructure that will support research relevant to cell–matrix interactions in disease progression, tissue repair and regeneration, and v) provide access to instrumentation and technical support. A Pilot Project program provides funding to investigators who propose applying their expertise to matrix biology questions. Support from the National Institute of General Medical Sciences at the National Institutes of Health that established the Center of Biomedical Research Excellence in Matrix Biology has significantly enhanced the infrastructure and the capabilities of researchers at Boise State University, leading to new approaches that address disease diagnosis, prevention, and treatment. New multidisciplinary collaborations have been formed with investigators who may not have previously considered how their biomedical research programs addressed fundamental and applied questions involving the extracellular matrix. Collaborations with the broader matrix biology community are encouraged.
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Laudel, Grit, and Jana Bielick. "The Emergence of Individual Research Programs in the Early Career Phase of Academics." Science, Technology, & Human Values 43, no. 6 (March 19, 2018): 972–1010. http://dx.doi.org/10.1177/0162243918763100.

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Scientific communities expect early career researchers (ECRs) to become intellectually independent and to develop longer-term research plans (individual research programs [IRPs]). How such programs emerge during the early career phase is still poorly understood. Drawing on semistructured interviews with German ECRs in plant biology, experimental physics, and early modern history, we show that the development of such a plan is a research process in itself. The processes leading to IRPs are conditioned by the fields’ epistemic practices for producing new knowledge. By linking the conditions under which ECRs work to the epistemic properties of their IRPs, we identify mechanisms that produce these programs and conditions facilitating or hindering the operation of these mechanisms.
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Kowalski, Charles J. "Data Analysis in Craniofacial Biology with Special Emphasis on Longitudinal Studies." Cleft Palate-Craniofacial Journal 30, no. 2 (March 1993): 111–20. http://dx.doi.org/10.1597/1545-1569_1993_030_0111_daicbw_2.3.co_2.

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Recommendations are made for strengthening data description and analysis in craniofacial biology. Special emphasis is placed on longitudinal data, and PC programs for accomplishing appropriate analyses in this context are described and made available to interested readers. Some more general recommendations are treated in less detail. These include the effective description of data using stem-and-leaf displays and/or boxplots, the use of decision-analytic methods in the management of patients with dentofacial deformities, and the valid application of certain statistical methods in single-subject studies. Finally, it is conjectured that computer-intensive methods such as randomization tests and jackknifing will play an increasingly prominent role in craniofacial research.
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Looney, C. R., and J. H. Pryor. "Practical applications of new research information in the practice of bovine embryo transfer." Reproduction, Fertility and Development 22, no. 1 (2010): 145. http://dx.doi.org/10.1071/rd09223.

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For more than 40 years, practitioners have sought to improve all aspects of commercial bovine embryo transfer. The development of new technologies for this industry has been substantial, with recent focus on cryopreservation techniques and the in vitro production of embryos fertilised with sexed spermatozoa. When these and other new technologies are developed, the following questions remain: (1) is said technology regulated or does it require licensing; and (2) is it applicable and, if so, is it financially feasible? Computer access to published research and the advancement of data software programs conducive to the industry for data procurement have been essential for helping practitioners answer these questions by enhancing their ability to analyse and apply data. The focus of the present paper is to aid commercial embryo transfer practitioners in determining new technologies that are available and whether they can be implemented effectively, benefiting their programs.
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Sipper, Moshe. "Fifty Years of Research on Self-Replication: An Overview." Artificial Life 4, no. 3 (July 1998): 237–57. http://dx.doi.org/10.1162/106454698568576.

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The study of artificial self-replicating structures or machines has been taking place now for almost half a century. My goal in this article is to present an overview of research carried out in the domain of self-replication over the past 50 years, starting from von Neumann's work in the late 1940s and continuing to the most recent research efforts. I shall concentrate on computational models, that is, ones that have been studied from a computer science point of view, be it theoretical or experimental. The systems are divided into four major classes, according to the model on which they are based: cellular automata, computer programs, strings (or strands), or an altogether different approach. With the advent of new materials, such as synthetic molecules and nanomachines, it is quite possible that we shall see this somewhat theoretical domain of study producing practical, real-world applications.
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KEARNEY, P., and P. THIBAULT. "BIOINFORMATICS MEETS PROTEOMICS — BRIDGING THE GAP BETWEEN MASS SPECTROMETRY DATA ANALYSIS AND CELL BIOLOGY." Journal of Bioinformatics and Computational Biology 01, no. 01 (April 2003): 183–200. http://dx.doi.org/10.1142/s021972000300023x.

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Proteomics research programs typically comprise the identification of protein content of any given cell, their isoforms, splice variants, post-translational modifications, interacting partners and higher-order complexes under different conditions. These studies present significant analytical challenges owing to the high proteome complexity and the low abundance of the corresponding proteins, which often requires highly sensitive and resolving techniques. Mass spectrometry plays an important role in proteomics and has become an indispensable tool for molecular and cellular biology. However, the analysis of mass spectrometry data can be a daunting task in view of the complexity of the information to decipher, the accuracy and dynamic range of quantitative analysis, the availability of appropriate bioinformatics software and the overwhelming size of data files. The past ten years have witnessed significant technological advances in mass spectrometry-based proteomics and synergy with bioinformatics is vital to fulfill the expectations of biological discovery programs. We present here the technological capabilities of mass spectrometry and bioinformatics for mining the cellular proteome in the context of discovery programs aimed at trace-level protein identification and expression from microgram amounts of protein extracts from human tissues.
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Dissertations / Theses on the topic "Biology Research Computer programs"

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Kiehl, Debra Elisabeth. "A comparison of traditional animal dissection and computer simulation dissection." CSUSB ScholarWorks, 2007. https://scholarworks.lib.csusb.edu/etd-project/3247.

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Iturrioz, Amaia Bernaras. "A method for understanding experimental computer programs in artificial intelligence research." Thesis, University of Edinburgh, 1993. http://hdl.handle.net/1842/20026.

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This thesis is concerned with the use of Software Engineering abstraction constructs to help in the process of understanding computer programs that are built as part of experiments in the Symbolic Paradigm. It is also concerned with developing and testing a method to analyse these programs in an organised and structured way. In a series of three experiments, the use of abstraction constructs to help the process of transforming a program to a more abstract form, and how to do this in a structured way, was incrementally investigated. This involved first exploring the use of abstraction constructs to achieve higher degrees of abstraction in a small example; the next step was to use the understanding of their use and of how to transform a program in a bigger exanple, from which a more clearly defined role of the abstraction constructs, and an initial scheme for transforming a program, was achieved; the last step involved investigating a complete form of an analysis procedure to analyse experimental programs built by incremental prototying, and that is supported by the use of abstraction constructs. The result is the Prototype Analysis Method (PAM): a static analysis method to help in the understanding of incrementally built experimental computer programs in AI. An essential part of this method is a transformation process that is supported by the use of Software Engineering abstraction constructs, and of test sets from dynamic analysis for validation. This research clearly demonstrates the successful application of Software Engineering abstraction constructs is an important aspect of AI research. Results from this research also point to further interesting issues such as the relation between Knowledge Level descriptions and abstract Symbol Level descriptions.
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Joseph, Arokiya Louis Monica. "Sequence Similarity Search portal." CSUSB ScholarWorks, 2007. https://scholarworks.lib.csusb.edu/etd-project/3124.

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This project brings the bioinformatics community a new development concept in which users can access all data and applications hosted in the main research centers as if they were installed on their local machines, providing seamless integration between disparate services. The project moves to integrate the sequence similarity searching at EBI and NCBI by using web services. It also intends to allow molecular biologists to save their searches and act as a log book for their sequence similarity searches. The project will also allow the biologists to share their sequences and results with others.
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Rahim, Humaira. "Athena: An online proposal development system." CSUSB ScholarWorks, 2005. https://scholarworks.lib.csusb.edu/etd-project/2856.

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Athena - Online Proposal Development System was the first version of a vision of Dr. Richard Botting, Professor, Department of Computer Science at California State University, San Bernardino. The program, a JSP based system incorporating a MySql database, moves the writing, review, and annotation of project proposals into the digital environment. It allows Computer Science Master's students to provide their project proposals online for review and annotation by the committee members.
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McIntosh, Cecilia A. "Building and Sustaining Research at East Tennessee State University." Digital Commons @ East Tennessee State University, 2012. https://dc.etsu.edu/etsu-works/366.

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Beyers, Ronald Noel. "Selecting educational computer software and evaluating its use, with special reference to biology education." Thesis, Rhodes University, 1992. http://hdl.handle.net/10962/d1003649.

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In the field of Biology there is a reasonable amount of software available for educational use but in the researcher's experience there are few teachers who take the computer into the classroom/laboratory, Teachers will make use of video machines and tape recorders quite happily, but a computer is a piece of apparatus which they are not prepared to use in the classroom/laboratory. This thesis is an attempt to devise an educational package, consisting of a Selection Form and an Evaluation Form, which can be used by teachers to select and evaluate educational software in the field of Biology. The forms were designed specifically for teachers to use in preparation of a computer lesson. The evaluation package also provides the teacher with a means of identifying whether the lesson has achieved its objectives or not. The teacher may also be provided with feedback about the lesson. The data is gathered by means of a questionnaire which the pupils complete. It would appear that teachers are uncertain as regards the purchase of software for their subject from the many catalogues that are available. The evaluation package implemented in this research can be regarded as the beginnings of a data base for the accumulation of information to assist teachers with details on which software to select. Evidence is provided in this thesis for the practical application of the Selection and Evaluation Forms, using Biology software.
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Lira, Bonates Eduardo Jorge. "Analysis of truckshovel dispatching policies using computer simulation." Thesis, McGill University, 1986. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=65406.

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Chen, Kun-Che. "Extending the solicitation management system: User interface improvement and system administration support." CSUSB ScholarWorks, 2008. https://scholarworks.lib.csusb.edu/etd-project/3398.

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The main purpose of this project is to develop new functionalities for the Solicitation Management System (SMS) to support the Office of Technology Transfer and Commercialization (OTTC), California State University San Bernardino (CSUSB) and the Center for the Commercialization of Advanced Technology (CCAT), San Diego State University (SDSU) for the 2008 solicitation, which opened on 28 Jan 2008. SMS is a system built to facilitate the processing of grant proposal solicitations. The SMS was first built in 2004 and was primarily used by the OTTC, CSUSB for its solicitation activities. The new version of the SMS is more user friendly, so that it is easier for users to use and comprehend. The purpose of this software is to aid the processing of a solicitation for organizations that conduct solicitations for grant proposals.
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Beedell, David C. (David Charles). "The effect of sampling error on the interpretation of a least squares regression relating phosporus and chlorophyll." Thesis, McGill University, 1995. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=22720.

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Least squares linear regression is a common tool in ecological research. One of the central assumptions of least squares linear regression is that the independent variable is measured without error. But this variable is measured with error whenever it is a sample mean. The significance of such contraventions is not regularly assessed in ecological studies. A simulation program was made to provide such an assessment. The program requires a hypothetical data set, and using estimates of S$ sp2$ it scatters the hypothetical data to simulate the effect of sampling error. A regression line is drawn through the scattered data, and SSE and r$ sp2$ are measured. This is repeated numerous times (e.g. 1000) to generate probability distributions for r$ sp2$ and SSE. From these distributions it is possible to assess the likelihood of the hypothetical data resulting in a given SSE or r$ sp2$. The method was applied to survey data used in a published TP-CHLa regression (Pace 1984). Beginning with a hypothetical, linear data set (r$ sp2$ = 1), simulated scatter due to sampling exceeded the SSE from the regression through the survey data about 30% of the time. Thus chances are 3 out of 10 that the level of uncertainty found in the surveyed TP-CHLa relationship would be observed if the true relationship were perfectly linear. If this is so, more precise and more comprehensive models will only be possible when better estimates of the means are available. This simulation approach should apply to all least squares regression studies that use sampled means, and should be especially relevant to studies that use log-transformed values.
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Gregory, Victor Paul. "Monte Carlo computer simulation of sub-critical Lennard-Jones particles." Thesis, This resource online, 1991. http://scholar.lib.vt.edu/theses/available/etd-11242009-020125/.

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Books on the topic "Biology Research Computer programs"

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McCloskey, Moya. QUERCUS: Statistics for bioscientists : a student guidebook. London: Arnold, 1997.

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National Research Council (U.S.). Committee on Space Biology and Medicine. Assessment of programs in space biology and medicine. Washington, DC: National Academy Press, 1991.

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National Institutes of Health (U.S.). Review of the National Institutes of Health biomedical research training programs. Bethesda, Maryland: [National Institutes of Health, National Heart, Lung, and Blood Institute], 1989.

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United States. Department of Energy. Health and Environmental Research Advisory Committee. The application of genome and structural biology programs. Washington, D.C.]: The Department, 1995.

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Abramson, J. H. Computer programs for epidemiologists: PEPI version 4.0. Salt Lake City: Sagebrush Press, 2001.

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Rawlings, C. J. Software directory for molecular biologists. (Basingstoke): Macmillan, 1986.

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Statistics for social research. Basingstoke: Macmillan, 1997.

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Luqi. Research directions in software analysis, synthesis and certification. Monterey, Calif: Naval Postgraduate School, 1992.

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Valkó, Péter. Advanced scientific computing in BASIC with applications in chemistry, biology and pharmacology. Amsterdam: Elsevier, 1989.

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1949-, Vajda Sándor, ed. Advanced scientific computing in BASIC: With applications in chemistry, biology, and pharmacology. Amsterdam: Elsevier, 1989.

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Book chapters on the topic "Biology Research Computer programs"

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Ehsani, Sepehr. "Analytic Philosophy for Biomedical Research: The Imperative of Applying Yesterday’s Timeless Messages to Today’s Impasses." In Future of Business and Finance, 167–200. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-41309-5_13.

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AbstractThe mantra that “the best way to predict the future is to invent it” (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word “theory”) as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined.
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Byrne, Barbara M. "Selecting Sem Computer Programs." In Handbook of Quantitative Methods for Educational Research, 367–94. Rotterdam: SensePublishers, 2013. http://dx.doi.org/10.1007/978-94-6209-404-8_17.

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Raoprasert, Tanachart, and Sardar M. N. Islam. "Methodology, Research Process, and Computer Programs." In Designing an Efficient Management System, 63–94. Heidelberg: Physica-Verlag HD, 2010. http://dx.doi.org/10.1007/978-3-7908-2372-1_4.

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Loison, Laurent, and Emily Herring. "Lamarckian Research Programs in French Biology (1900–1970)." In The Darwinian Tradition in Context, 243–69. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-69123-7_11.

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Appleget, Jeffrey A., and R. Kevin Wood. "Explicit-Constraint Branching for Solving Mixed-Integer Programs." In Operations Research/Computer Science Interfaces Series, 245–61. Boston, MA: Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4567-5_14.

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McCourt, Robert P. "Computer Utilization in Artemia Research." In Cell and Molecular Biology of Artemia Development, 439–40. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-0004-6_47.

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Rea, Giuseppina, Amina Antonacci, Maya Lambreva, Andrea Margonelli, Cecilia Ambrosi, and Maria Teresa Giardi. "The NUTRA-SNACKS Project: Basic Research and Biotechnological Programs on Nutraceutics." In Advances in Experimental Medicine and Biology, 1–16. Boston, MA: Springer US, 2010. http://dx.doi.org/10.1007/978-1-4419-7347-4_1.

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Bjørn, Pernille, Maria Menendez-Blanco, and Valeria Borsotti. "FemTech.dk Research Initiative." In Diversity in Computer Science, 9–12. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-13314-5_2.

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AbstractFemTech.dk is situated in the Department of Computer Science at University of Copenhagen Denmark and has been an ongoing inquiry into the specific circumstances within computer science that produce gender imbalance and includes activities dedicated to making a change through design interventions. FemTech.dk was created in 2016 to engage with research within gender and diversity and to explore the role of gender equity as part of digital technology design and development. FemTech.dk considers how and why computer science as a field and profession in Denmark has such a distinct unbalanced gender representation in the twenty-first century. The focus was initially on the student base of the bachelor’s program in computer science, which from the 1980s until 2016 was remarkably smaller than for other science programs at the University of Copenhagen. In terms of numbers, only 15 women students entered the bachelor’s degree program in 2012 and 2013, and only 12 women students entered the program in 2014. In each of these 3 years, more than 160 students entered the program in total. Reviewing the 15-year period 2000–2014, the share of women students in the program was 7–9%, the lowest percentage of women in a study program across all of the University of Copenhagen. To compare, in 2016 the share of women students in the Math program was 30%, and in Physics was 25%.
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Thomas, Michael A., Mitch D. Day, and Luobin Yang. "Computational Options for Bioinformatics Research in Evolutionary Biology." In Lecture Notes in Computer Science, 68–75. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11428848_9.

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Gasparini, Isabela, Simone Diniz Junqueira Barbosa, Milene Selbach Silveira, Sílvia Amélia Bim, and Clodis Boscarioli. "How Does HCI Research Affect Education Programs? A Study in the Brazilian Context." In Human-Computer Interaction – INTERACT 2015, 592–610. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-22668-2_46.

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Conference papers on the topic "Biology Research Computer programs"

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Chaudhary, Niharika, and Sanjay Saini. "A Progress on Protein Structure Prediction using Various Soft Computing Techniques." In 9th International Conference on Computer Science and Information Technology (CSIT 2022). Academy and Industry Research Collaboration Center (AIRCC), 2022. http://dx.doi.org/10.5121/csit.2022.121410.

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In molecular and computational biology, predicting the three-dimensional structure of a protein from its amino acid sequence has long been an outstanding goal. Soft computing techniques for solving protein structure prediction problems have been gaining the attention of researchers because of their capacity to accommodate imprecision and uncertainty in vast and complicated search spaces. This paper provides a comprehensive overview of recent protein structure prediction efforts and progress using various soft computing techniques. This paper summarises key research in the field of protein structure prediction that has been published in the recent decade. Despite significant research efforts in recent decades, there is still a lot of room for improvement in this field.
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HALSTEAD, T., and R. KRAUSS. "The rationale for fundamental research in space biology - Introduction and background." In Space Programs and Technologies Conference. Reston, Virigina: American Institute of Aeronautics and Astronautics, 1992. http://dx.doi.org/10.2514/6.1992-1342.

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LEWIS, NORMAN, and CLARENCE RYAN. "Research in molecular biology - Realizing the potential of microgravity in biological systems." In Space Programs and Technologies Conference. Reston, Virigina: American Institute of Aeronautics and Astronautics, 1992. http://dx.doi.org/10.2514/6.1992-1347.

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Lipnitski, L. A., P. K. Shalkevich, M. A. Treyvas, and E. P. Cherevan. "RESEARCH AND COMPARISON OF OPTIMIZATION OF COMPUTER PROGRAMS." In SAKHAROV READINGS 2021: ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. International Sakharov Environmental Institute of Belarusian State University, 2021. http://dx.doi.org/10.46646/sakh-2021-2-302-305.

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Improving the performance of the created software product is one of the most important moments in the information industry. Optimal values of the speed of the program are achieved using various methods of code optimization. This paper presents the main ways to solve this problem.
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Huggard, Meriel, and Ciaran Mc Goldrick. "Formalising research methods for graduate programs in computer science." In 2007 37th Annual Frontiers in Education Conference - Global Engineering: Knowledge Without Borders, Opportunities Without Passports. IEEE, 2007. http://dx.doi.org/10.1109/fie.2007.4418118.

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Jeuring, Johan, L. Thomas van Binsbergen, Alex Gerdes, and Bastiaan Heeren. "Model solutions and properties for diagnosing student programs in Ask-Elle." In the Computer Science Education Research Conference. New York, New York, USA: ACM Press, 2014. http://dx.doi.org/10.1145/2691352.2691355.

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MacKellar, Bonnie, Gregory Hislop, Mihaela Sabin, and Amber Settle. "Information Technology and Computer Science Programs." In SIGITE/RIIT '15: The 16th Annual Conference on Information Technology Education and the 4th Annual Conference on Research in Information Technology. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2808006.2808014.

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Godfrey, Brendan B. "Some particle beam computer programs adapted from plasma physics research." In AIP Conference Proceedings Volume 177. AIP, 1988. http://dx.doi.org/10.1063/1.37818.

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McPherson, Jeffrey D., Ian R. Grosse, Sundar Krishnamurty, Jack C. Wileden, Elizabeth R. Dumont, and Michael A. Berthaume. "Integrating Biological and Engineering Ontologies." 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/detc2013-13527.

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As methods for engineering data acquisition improve, methods for storing, generating knowledge from, and sharing that data for efficient reuse have become more important. Knowledge management in the engineering community can greatly benefit from advancements made in knowledge management in biology. The biological community has already made progress in knowledge management through projects such as the Gene Ontology and CellML, and it behooves the engineering community to learn from their successes. Engineering and biology overlap in the field of biosimulation, (i.e. finite-element analysis of biological systems, see www.biomesh.org) which gives an opportunity to integrate successful ontologies from the biology community into the engineering community. Previous research has led to the creation of the Biomesh project, which is a collection of biological finite element (FE) models. These FE models relate to a particular anatomical structure of an organism, and to the set of biological material properties associated with the models. Thus, knowledge management for this application requires knowledge integration from three distinct fields: engineering (materials and models), anatomy, and biological classification. The existing e-Design Framework offers the Engineering Analysis Models ontology and Materials ontology to store knowledge about materials and FE models. Similarly, the existing Minimal Anatomical Terms ontology and the NCBI Organismal Classification taxonomy were used to store information about anatomy and biological classification, respectively. In this paper these ontologies are interlinked in a single, synergistic ontology to expose and integrate knowledge in a transparent manner between previously disparate domains. A case study is presented to demonstrate the usefulness of the approach in which knowledge from a biological material and FE model are methodically stored in the new ontology, and the organismal classification and anatomical structure of the model are immediately exposed to the user.
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Mirza, Diba, Phillip Conrad, and Cynthia Lee. "Research Questions regarding Undergraduate TA and Mentor Programs in Computer Science." In SIGCSE '20: The 51st ACM Technical Symposium on Computer Science Education. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3328778.3372532.

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Reports on the topic "Biology Research Computer programs"

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Shani, Uri, Lynn Dudley, Alon Ben-Gal, Menachem Moshelion, and Yajun Wu. Root Conductance, Root-soil Interface Water Potential, Water and Ion Channel Function, and Tissue Expression Profile as Affected by Environmental Conditions. United States Department of Agriculture, October 2007. http://dx.doi.org/10.32747/2007.7592119.bard.

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Constraints on water resources and the environment necessitate more efficient use of water. The key to efficient management is an understanding of the physical and physiological processes occurring in the soil-root hydraulic continuum.While both soil and plant leaf water potentials are well understood, modeled and measured, the root-soil interface where actual uptake processes occur has not been sufficiently studied. The water potential at the root-soil interface (yᵣₒₒₜ), determined by environmental conditions and by soil and plant hydraulic properties, serves as a boundary value in soil and plant uptake equations. In this work, we propose to 1) refine and implement a method for measuring yᵣₒₒₜ; 2) measure yᵣₒₒₜ, water uptake and root hydraulic conductivity for wild type tomato and Arabidopsis under varied q, K⁺, Na⁺ and Cl⁻ levels in the root zone; 3) verify the role of MIPs and ion channels response to q, K⁺ and Na⁺ levels in Arabidopsis and tomato; 4) study the relationships between yᵣₒₒₜ and root hydraulic conductivity for various crops representing important botanical and agricultural species, under conditions of varying soil types, water contents and salinity; and 5) integrate the above to water uptake term(s) to be implemented in models. We have made significant progress toward establishing the efficacy of the emittensiometer and on the molecular biology studies. We have added an additional method for measuring ψᵣₒₒₜ. High-frequency water application through the water source while the plant emerges and becomes established encourages roots to develop towards and into the water source itself. The yᵣₒₒₜ and yₛₒᵢₗ values reflected wetting and drying processes in the rhizosphere and in the bulk soil. Thus, yᵣₒₒₜ can be manipulated by changing irrigation level and frequency. An important and surprising finding resulting from the current research is the obtained yᵣₒₒₜ value. The yᵣₒₒₜ measured using the three different methods: emittensiometer, micro-tensiometer and MRI imaging in both sunflower, tomato and corn plants fell in the same range and were higher by one to three orders of magnitude from the values of -600 to -15,000 cm suggested in the literature. We have added additional information on the regulation of aquaporins and transporters at the transcript and protein levels, particularly under stress. Our preliminary results show that overexpression of one aquaporin gene in tomato dramatically increases its transpiration level (unpublished results). Based on this information, we started screening mutants for other aquaporin genes. During the feasibility testing year, we identified homozygous mutants for eight aquaporin genes, including six mutants for five of the PIP2 genes. Including the homozygous mutants directly available at the ABRC seed stock center, we now have mutants for 11 of the 19 aquaporin genes of interest. Currently, we are screening mutants for other aquaporin genes and ion transporter genes. Understanding plant water uptake under stress is essential for the further advancement of molecular plant stress tolerance work as well as for efficient use of water in agriculture. Virtually all of Israel’s agriculture and about 40% of US agriculture is made possible by irrigation. Both countries face increasing risk of water shortages as urban requirements grow. Both countries will have to find methods of protecting the soil resource while conserving water resources—goals that appear to be in direct conflict. The climate-plant-soil-water system is nonlinear with many feedback mechanisms. Conceptual plant uptake and growth models and mechanism-based computer-simulation models will be valuable tools in developing irrigation regimes and methods that maximize the efficiency of agricultural water. This proposal will contribute to the development of these models by providing critical information on water extraction by the plant that will result in improved predictions of both water requirements and crop yields. Plant water use and plant response to environmental conditions cannot possibly be understood by using the tools and language of a single scientific discipline. This proposal links the disciplines of soil physics and soil physical chemistry with plant physiology and molecular biology in order to correctly treat and understand the soil-plant interface in terms of integrated comprehension. Results from the project will contribute to a mechanistic understanding of the SPAC and will inspire continued multidisciplinary research.
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Bilousova, Liudmyla I., Liudmyla E. Gryzun, Daria H. Sherstiuk, and Ekaterina O. Shmeltser. Cloud-based complex of computer transdisciplinary models in the context of holistic educational approach. [б. в.], September 2019. http://dx.doi.org/10.31812/123456789/3259.

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The paper represents the authors’ cloud-based complex of computer dynamic models and their transdisciplinary facilities. Proper theoretical background for the complex design is elaborated and the process of the computer models development is covered. The models in the complex are grouped in the sections according to the curriculum subjects (Physics, Algebra, Geometry, Biology, Geography, and Informatics). Each of the sections includes proper models along with their description and transdisciplinary didactic support. The paper also presents recommendations as for using of the complex to provide holistic learning of Mathematics, Science and Informatics at secondary school. The prospects of further research are outlined.
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Oleksiuk, Vasyl P., and Olesia R. Oleksiuk. Exploring the potential of augmented reality for teaching school computer science. [б. в.], November 2020. http://dx.doi.org/10.31812/123456789/4404.

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The article analyzes the phenomenon of augmented reality (AR) in education. AR is a new technology that complements the real world with the help of computer data. Such content is tied to specific locations or activities. Over the last few years, AR applications have become available on mobile devices. AR becomes available in the media (news, entertainment, sports). It is starting to enter other areas of life (such as e-commerce, travel, marketing). But education has the biggest impact on AR. Based on the analysis of scientific publications, the authors explored the possibilities of using augmented reality in education. They identified means of augmented reality for teaching computer science at school. Such programs and services allow students to observe the operation of computer systems when changing their parameters. Students can also modify computer hardware for augmented reality objects and visualize algorithms and data processes. The article describes the content of author training for practicing teachers. At this event, some applications for training in AR technology were considered. The possibilities of working with augmented reality objects in computer science training are singled out. It is shown that the use of augmented reality provides an opportunity to increase the realism of research; provides emotional and cognitive experience. This all contributes to engaging students in systematic learning; creates new opportunities for collaborative learning, develops new representations of real objects.
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Savosko, V., I. Komarova, Yu Lykholat, E. Yevtushenko, and T. Lykholat. Predictive model of heavy metals inputs to soil at Kryvyi Rih District and its use in the training for specialists in the field of Biology. IOP Publishing, 2021. http://dx.doi.org/10.31812/123456789/4511.

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The importance of our research is due to the need to introduce into modern biological education methods of predictive modeling which are based on relevant factual material. Such an actual material may be the entry of natural and anthropic heavy metals into the soil at industrial areas. The object of this work: (i) to work out a predictive model of the total heavy metals inputs to soil at the Kryvyi Rih ore-mining & metallurgical District and (ii) to identify ways to use this model in biological education. Our study areas are located in the Kryvyi Rih District (Dnipropetrovsk region, Central Ukraine). In this work, classical scientific methods (such as analysis and synthesis, induction and deduction, analogy and formalization, abstraction and concretization, classification and modelling) were used. By summary the own research results and available scientific publications, the heavy metals total inputs to soils at Kryvyi Rih District was predicted. It is suggested that the current heavy metals content in soils of this region due to 1) natural and 2) anthropogenic flows, which are segmented into global and local levels. Predictive calculations show that heavy metals inputs to the soil of this region have the following values (mg ⋅ m2/year): Fe – 800-80 000, Mn – 125-520, Zn – 75-360, Ni – 20-30, Cu – 15-50, Pb – 7.5-120, Cd – 0.30-0.70. It is established that anthropogenic flows predominate in Fe and Pb inputs (60-99 %), natural flows predominate in Ni and Cd inputs (55-95 %). While, for Mn, Zn, and Cu inputs the alternate dominance of natural and anthropogenic flows are characterized. It is shown that the predictive model development for heavy metals inputs to soils of the industrial region can be used for efficient biological education (for example in bachelors of biologists training, discipline "Computer modelling in biology").
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Савосько, Василь Миколайович, Ірина Олександрівна Комарова, Юрій Васильович Лихолат, Едуард Олексійович Євтушенко,, and Тетяна Юріївна Лихолат. Predictive Model of Heavy Metals Inputs to Soil at Kryvyi Rih District and its Use in the Training for Specialists in the Field of Biology. IOP Publishing, 2021. http://dx.doi.org/10.31812/123456789/4266.

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The importance of our research is due to the need to introduce into modern biological education methods of predictive modeling which are based on relevant factual material. Such an actual material may be the entry of natural and anthropic heavy metals into the soil at industrial areas. The object of this work: (i) to work out a predictive model of the total heavy metals inputs to soil at the Kryvyi Rih ore-mining & metallurgical District and (ii) to identify ways to use this model in biological education. Our study areas are located in the Kryvyi Rih District (Dnipropetrovsk region, Central Ukraine). In this work, classical scientific methods (such as analysis and synthesis, induction and deduction, analogy and formalization, abstraction and concretization, classification and modelling) were used. By summary the own research results and available scientific publications, the heavy metals total inputs to soils at Kryvyi Rih District was predicted. It is suggested that the current heavy metals content in soils of this region due to 1) natural and 2) anthropogenic flows, which are segmented into global and local levels. Predictive calculations show that heavy metals inputs to the soil of this region have the following values ( mg ∙ m ଶ year ⁄ ): Fe – 800-80 000, Mn – 125-520, Zn – 75-360, Ni – 20-30, Cu – 15-50, Pb – 7.5-120, Cd – 0.30-0.70. It is established that anthropogenic flows predominate in Fe and Pb inputs (60-99 %), natural flows predominate in Ni and Cd inputs (55-95 %). While, for Mn, Zn, and Cu inputs the alternate dominance of natural and anthropogenic flows are characterized. It is shown that the predictive model development for heavy metals inputs to soils of the industrial region can be used for efficient biological education (for example in bachelors of biologists training, discipline “Computer modelling in biology”).
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Valko, Nataliia V., Viacheslav V. Osadchyi, and Vladyslav S. Kruhlyk. Cloud resources use for students' project activities. [б. в.], June 2021. http://dx.doi.org/10.31812/123456789/4444.

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The modern educational system proclaims learning aimed at acquiring practical skills and based on the activity approach. Educational research projects are the necessary component of curricula in physics, computer science, biology and chemistry. There is a problem of specialized equipment and facilities using for the implementation of such projects in distance learning. Therefore, the issue of cloud resources using for distance learning organization in robotics is relevant. The article presents a brief overview of the current state of projects development in Ukrainian schools and approaches used in foreign educational institutions in teaching robotics distantly. The article describes the stages of robotics projects development such as organizational, communicative, project work, summarizing. The peculiarities of the stages in distance learning and the possibilities of cloud technologies in robotics are also considered. The authors’ experience in projects developing in this environment for students and future teachers is described.
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Twining, Benjamin S., Mak A. Saito, Alyson E. Santoro, Adrian Marchetti, and Naomi M. Levine. US National BioGeoSCAPES Workshop Report. Woods Hole Oceangraphic Institution, January 2023. http://dx.doi.org/10.1575/1912/29604.

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BioGeoSCAPES (BGS) is an international program being developed to understand controls on ocean productivity and metabolism by integrating systems biology (‘omics) and biogeochemistry (Figure 1). To ensure global input into the design of the BGS Program, countries interested in participating were tasked with holding an organizing meeting to discuss the country-specific research priorities. A United States BGS planning meeting, sponsored by the Ocean Carbon & Biogeochemistry (OCB) Project Office, was convened virtually November 10-12, 2021. The objectives of the meeting were to communicate the planning underway by international partners, engage the US community to explore possible national contributions to such a program, and build understanding, support, and momentum for US efforts towards BGS. The meeting was well-attended, with 154 participants and many fruitful discussions that are summarized in this document. Key outcomes from the meeting were the identification of additional programs and partners for BGS, a prioritization of measurements requiring intercalibration, and the development of a consensus around key considerations to be addressed in a science plan. Looking forward, the hope is that this workshop will serve as the foundation for future US and international discussions and planning for a BGS program, enabled by NSF funding for an AccelNet project (AccelNet - Implementation: Development of an International Network for the Study of Ocean Metabolism and Nutrient Cycles on a Changing Planet (BioGeoSCAPES)), beginning in 2022.
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Холошин, Ігор Віталійович, Ірина Миколаївна Варфоломєєва, Олена Вікторівна Ганчук, Ольга Володимирівна Бондаренко, and Андрій Валерійович Пікільняк. Pedagogical techniques of Earth remote sensing data application into modern school practice. CEUR-WS.org, 2018. http://dx.doi.org/10.31812/123456789/3257.

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Abstract. The article dwells upon the Earth remote sensing data as one of the basic directions of Geo-Information Science, a unique source of information on processes and phenomena occurring in almost all spheres of the Earth geographic shell (atmosphere, hydrosphere, lithosphere, etc.). The authors argue that the use of aerospace images by means of the information and communication technologies involvement in the learning process allows not only to increase the information context value of learning, but also contributes to the formation of students’ cognitive interest in such disciplines as geography, biology, history, physics, computer science, etc. It has been grounded that remote sensing data form students’ spatial, temporal and qualitative concepts, sensory support for the perception, knowledge and explanation of the specifics of objects and phenomena of geographical reality, which, in its turn, provides an increase in the level of educational achievements. The techniques of aerospace images application into the modern school practice have been analyzed and illustrated in the examples: from using them as visual aids, to realization of practical and research orientation of training on the basis of remote sensing data. Particular attention is paid to the practical component of the Earth remote sensing implementation into the modern school practice with the help of information and communication technologies.
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Kholoshyn, Ihor V., Iryna M. Varfolomyeyeva, Olena V. Hanchuk, Olga V. Bondarenko, and Andrey V. Pikilnyak. Pedagogical techniques of Earth remote sensing data application into modern school practice. [б. в.], September 2019. http://dx.doi.org/10.31812/123456789/3262.

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The article dwells upon the Earth remote sensing data as one of the basic directions of Geo-Information Science, a unique source of information on processes and phenomena occurring in almost all spheres of the Earth geographic shell (atmosphere, hydrosphere, lithosphere, etc.). The authors argue that the use of aerospace images by means of the information and communication technologies involvement in the learning process allows not only to increase the information context value of learning, but also contributes to the formation of students’ cognitive interest in such disciplines as geography, biology, history, physics, computer science, etc. It has been grounded that remote sensing data form students’ spatial, temporal and qualitative concepts, sensory support for the perception, knowledge and explanation of the specifics of objects and phenomena of geographical reality, which, in its turn, provides an increase in the level of educational achievements. The techniques of aerospace images application into the modern school practice have been analyzed and illustrated in the examples: from using them as visual aids, to realization of practical and research orientation of training on the basis of remote sensing data. Particular attention is paid to the practical component of the Earth remote sensing implementation into the modern school practice with the help of information and communication technologies.
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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.

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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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