BIO's Plan to Promote Opportunity and Access for the Underserved
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Redesigning the Eterna100 for the Vienna 2 Folding Engine
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.26.457839; this version posted August 28, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Redesigning the Eterna100 for the Vienna 2 folding engine Rohan V. Koodli1,*, Boris Rudolfs2,*, Hannah K. Wayment-Steele3, Eterna Structure Designersγ, Rhiju Das4,5,^ 1Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720 2Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92110 3Department of Chemistry, Stanford University, Stanford, CA 94305 4Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5Department of Physics, Stanford University, Stanford, CA 94305 *Indicates equal contribution γ Group Author: Membership of Eterna participants and list of player names is provided in Acknowledgments ^Corresponding Author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.08.26.457839; this version posted August 28, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract The rational design of RNA is becoming important for rapidly developing technologies in medicine and biochemistry. Recent work has led to the development of several RNA secondary structure design algorithms and corresponding benchmarks to evaluate their performance. However, the performance of these algorithms is linked to the nature of the underlying algorithms for predicting secondary structure from sequences. -
A Neuroevolution Approach to Imitating Human-Like Play in Ms
A Neuroevolution Approach to Imitating Human-Like Play in Ms. Pac-Man Video Game Maximiliano Miranda, Antonio A. S´anchez-Ruiz, and Federico Peinado Departamento de Ingenier´ıadel Software e Inteligencia Artificial Universidad Complutense de Madrid c/ Profesor Jos´eGarc´ıaSantesmases 9, 28040 Madrid (Spain) [email protected] - [email protected] - [email protected] http://www.narratech.com Abstract. Simulating human behaviour when playing computer games has been recently proposed as a challenge for researchers on Artificial Intelligence. As part of our exploration of approaches that perform well both in terms of the instrumental similarity measure and the phenomeno- logical evaluation by human spectators, we are developing virtual players using Neuroevolution. This is a form of Machine Learning that employs Evolutionary Algorithms to train Artificial Neural Networks by consider- ing the weights of these networks as chromosomes for the application of genetic algorithms. Results strongly depend on the fitness function that is used, which tries to characterise the human-likeness of a machine- controlled player. Designing this function is complex and it must be implemented for specific games. In this work we use the classic game Ms. Pac-Man as an scenario for comparing two different methodologies. The first one uses raw data extracted directly from human traces, i.e. the set of movements executed by a real player and their corresponding time stamps. The second methodology adds more elaborated game-level parameters as the final score, the average distance to the closest ghost, and the number of changes in the player's route. We assess the impor- tance of these features for imitating human-like play, aiming to obtain findings that would be useful for many other games. -
Poorna Roy Phd Dissertation
ANALYZING AND CLASSIFYING BIMOLECULAR INTERACTIONS: I. EFFECTS OF METAL BINDING ON AN IRON-SULFUR CLUSTER SCAFFOLD PROTEIN II. AUTOMATIC ANNOTATION OF RNA-PROTEIN INTERACTIONS FOR NDB Poorna Roy A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2017 Committee: Neocles Leontis, Committee Co-Chair Andrew Torelli, Committee Co-Chair Vipaporn Phuntumart, Graduate Faculty Representative H. Peter Lu © 2017 Poorna Roy All Rights Reserved iii ABSTRACT Neocles B. Leontis and Andrew T. Torelli, Committee co-chairs This dissertation comprises two distinct parts; however the different research agendas are thematically linked by their complementary approaches to investigate the nature of important intermolecular interactions. The first part is the study of interactions between an iron-sulfur cluster scaffold protein, IscU, and different transition metal ions. Interactions between IscU and specific metal ions are investigated and compared with those of SufU, a homologous Fe-S cluster biosynthesis protein from Gram-positive bacteria whose metal-dependent conformational behavior remains unclear. These studies were extended with additional metal ions selected to determine whether coordination geometry at the active sites of IscU and its homolog influence metal ion selectivity. Comparing the conformational behavior and affinity for different transition metal ions revealed that metal-dependent conformational transitions exhibited by IscU may be a recurring strategy exhibited by U-type proteins involved in Fe-S cluster biosynthesis. The second part of the thesis focuses on automated detection and annotation of specific interactions between nucleotides and amino acid residues in RNA-protein complexes. -
Designing Learning with Citizen Science and Games
The Emerging Learning Design Journal Volume 4 Issue 1 Article 3 February 2018 Designing Learning with Citizen Science and Games Karen Schrier Marist College Follow this and additional works at: https://digitalcommons.montclair.edu/eldj Part of the Curriculum and Instruction Commons Recommended Citation Schrier, Karen (2018) "Designing Learning with Citizen Science and Games," The Emerging Learning Design Journal: Vol. 4 : Iss. 1 , Article 3. Available at: https://digitalcommons.montclair.edu/eldj/vol4/iss1/3 This Trends is brought to you for free and open access by Montclair State University Digital Commons. It has been accepted for inclusion in The Emerging Learning Design Journal by an authorized editor of Montclair State University Digital Commons. For more information, please contact [email protected]. Volume 4 (2017) pp. 19-26 http://eldj.montclair.edu eld.j ISSN 2474-8218 Emerging Learning Design Journal Trend Designing Learning with Citizen Science and Games Karen Schrier Marist College [email protected] April 29, 2017 ABSTRACT This emerging trends article introduces concepts such as citizen science (the inclusion of non-professionals in scientific knowledge production) and knowledge games (games that enable players to solve real-world problems through crowdsourcing and collective intelligence activities within a game). The article shares the strengths and limitations of using citizen science and knowledge games in the classroom, as well as initial tips and guidelines for bringing these types of experiences to -
Geometric and Statistical Methods for the Analysis and Prediction of Structural Interactions Between Biomolecules Julie Bernauer
Geometric and statistical methods for the analysis and prediction of structural interactions between biomolecules Julie Bernauer To cite this version: Julie Bernauer. Geometric and statistical methods for the analysis and prediction of structural interac- tions between biomolecules. Bioinformatics [q-bio.QM]. Université Paris-Sud XI, 2015. tel-01136261 HAL Id: tel-01136261 https://tel.archives-ouvertes.fr/tel-01136261 Submitted on 26 Mar 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright Methodes´ geom´ etriques´ et statistiques pour l'analyse et la prediction´ des interactions structurales de biomolecules´ HABILITATION À DIRIGER DES RECHERCHES (Sp´ecialit´eInformatique) UNIVERSITÉ PARIS-SUD 11 pr´esent´eeet soutenue publiquement le 13 janvier 2015 Julie Bernauer Pr´esident: Philippe Dague Professeur, Universit´eParis Sud, LRI/LaDHAC Rapporteurs : Patrice Koehl Professor, University of California, Davis, Department of Computer Science Erik Lindahl Professor, KTH Royal Institute of Technology & Stockholm University, Department of Biochemistry -
Human Computation and Human Subject Tasks in Social Network Playful Applications
University of Bremen Doctoral Thesis Human Computation and Human Subject Tasks in Social Network Playful Applications Supervisors: Author: Dr. Rainer Malaka Aneta Takhtamysheva Dr. Andreas Breiter A thesis submitted in fulfilment of the requirements for the degree of Doctor of Engineering (Dr.-Ing.) in the Digital Media Mathematics and Informatics March 2016 Declaration of Authorship I, Aneta Takhtamysheva, declare that this thesis titled, ’Human Computation and Human Subject Tasks in Social Network Playful Applications’ and the work presented in it are my own. I confirm that: This work was done wholly or mainly while in candidature for a research degree at this University. Where any part of this thesis has previously been submitted for a degree or any other qualification at this University or any other institution, this has been clearly stated. Where I have consulted the published work of others, this is always clearly at- tributed. Where I have quoted from the work of others, the source is always given. With the exception of such quotations, this thesis is entirely my own work. I have acknowledged all main sources of help. Where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself. Signed: Date: ii UNIVERSITY OF BREMEN Abstract Mathematics and Informatics Doctor of Engineering (Dr.-Ing.) Human Computation and Human Subject Tasks in Social Network Playful Applications by Aneta Takhtamysheva Universal connectivity has made crowdsourcing - an online activity of a crowd toward the completion of a goal requested by someone in an open call - possible. -
RUSQ Vol. 58, No. 4
THE ALERT COLLECTOR Mark Shores, Editor Kristen Nyitray began her immersion in video games with an Atari 2600 and ColecoVision console and checking out Game On to games from her local public library. Later in life, she had the opportunity to start building a video game studies col- lection in her professional career as an archivist and special Game After collections librarian. While that project has since ended, you get the benefit of her expansive knowledge of video game sources in “Game On to Game After: Sources for Video Game Sources for Video History.” There is much in this column to help librarians wanting to support research in this important entertainment Game History form. Ready player one?—Editor ideo games have emerged as a ubiquitous and dominant form of entertainment as evidenced by statistics compiled in the United States and pub- lished by the Entertainment Software Association: V60 percent of Americans play video and/or computer games daily; 70 percent of gamers are 18 and older; the average age of a player is 34; adult women constitute 33 percent of play- ers; and sales in the United States were estimated in 2017 at $36 billion.1 What constitutes a video game? This seemingly simple question has spurred much technical and philosophical debate. To this point, in 2010 I founded with Raiford Guins (professor of cinema and media studies, the Media School, Kristen J. Nyitray Indiana University) the William A. Higinbotham Game Studies Collection (2010–2016), named in honor of physi- Kristen J. Nyitray is Director of Special Collections cist Higinbotham, developer of the analog computer game and University Archives, and University Archivist at Tennis for Two (as it is most commonly known).2 This game Stony Brook University, State University of New York. -
New Joysticks Available for Your Atari 2600
May Your Holiday Season Be a Classic One Classic Gamer Magazine Classic Gamer Magazine December 2000 3 The Xonox List 27 Teach Your Children Well 28 Games of Blame 29 Mit’s Revenge 31 The Odyssey Challenger Series 34 Interview With Bob Rosha 38 Atari Arcade Hits Review 41 Jaguar: Straight From the Cat’s 43 Mouth 6 Homebrew Review 44 24 Dear Santa 46 CGM Online Reset 5 22 So, what’s Happening with CGM Newswire 6 our website? Upcoming Releases 8 In the coming months we’ll Book Review: The First Quarter 9 be expanding our web pres- Classic Ad: “Fonz” from 1976 10 ence with more articles, games and classic gaming merchan- Lost Arcade Classic: Guzzler 11 dise. Right now we’re even The Games We Love to Hate 12 shilling Classic Gamer Maga- zine merchandise such as The X-Games 14 t-shirts and coffee mugs. Are These Games Unplayable? 16 So be sure to check online with us for all the latest and My Favorite Hedgehog 18 greatest in classic gaming news Ode to Arcade Art 20 and fun. Roland’s Rat Race for the C-64 22 www.classicgamer.com Survival Island 24 Head ‘em Off at the Past 48 Classic Ad: “K.C. Munchkin” 1982 49 My .025 50 Make it So, Mr. Borf! Dragon’s Lair 52 and Space Ace DVD Review How I Tapped Out on Tapper 54 Classifieds 55 Poetry Contest Winners 55 CVG 101: What I Learned Over 56 Summer Vacation Atari’s Misplays and Bogey’s 58 46 Deep Thaw 62 38 Classic Gamer Magazine December 2000 4 “Those who cannot remember the past are condemned to Issue 5 repeat it” - George Santayana December 2000 Editor-in-Chief “Unfortunately, those of us who do remember the past are Chris Cavanaugh condemned to repeat it with them." - unaccredited [email protected] Managing Editor -Box, Dreamcast, Play- and the X-Box? Well, much to Sarah Thomas [email protected] Station, PlayStation 2, the chagrin of Microsoft bashers Gamecube, Nintendo 64, everywhere, there is one rule of Contributing Writers Indrema, Nuon, Game business that should never be X Mark Androvich Boy Advance, and the home forgotten: Never bet against Bill. -
Building a Music Rhythm Video Game Information Systems and Computer
Building a music rhythm video game Ruben Rodrigues Rebelo Thesis to obtain the Master of Science Degree in Information Systems and Computer Engineering Supervisor: Prof. Rui Filipe Fernandes Prada Examination Committee Chairperson: Nuno Joao˜ Neves Mamede Supervisor: Prof. Rui Filipe Fernandes Prada Member of the Committee: Carlos Antonio´ Roque Martinho November 2016 Acknowledgments I would like to thank my supervisor, Prof. Rui Prada for the support and for making believe that my work in this thesis was not only possible, but also making me view that this work was important for myself. Also I want to thank Carla Boura Costa for helping me through this difficult stage and clarify my doubts that I was encountered this year. For the friends that I made this last year. Thank you to Miguel Faria, Tiago Santos, Nuno Xu, Bruno Henriques, Diogo Rato, Joana Condec¸o, Ana Salta, Andre´ Pires and Miguel Pires for being my friends and have the most interesting conversations (and sometimes funny too) that I haven’t heard in years. And a thank you to Vaniaˆ Mendonc¸a for reading my dissertation and suggest improvements. To my first friends that I made when I entered IST-Taguspark, thank you to Elvio´ Abreu, Fabio´ Alves and David Silva for your support. A small thank you to Prof. Lu´ısa Coheur for letting me and my origamis fill some of the space in the room of her students. A special thanks for Inesˆ Fernandes for inspire me to have the idea for the game of the thesis, and for giving special ideas that I wish to implement in a final version of the game. -
RNA Structure Through Multidimensional Chemical Mapping
REVIEW RNA structure through multidimensional chemical mapping Siqi Tian1 and Rhiju Das1,2* 1 Department of Biochemistry, Stanford University, Stanford, CA 94305, USA 2 Department of Physics, Stanford University, Stanford, CA 94305, USA Quarterly Reviews of Biophysics (2016), 49, e7, page 1 of 30 doi:10.1017/S0033583516000020 Abstract. The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire tran- scriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure deter- mination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed •OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to 200 nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM pro- tocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-cross-link-map (MXM) expansion to overcome this and other current limitations to resolving the in vivo ‘RNA structurome’. -
The History of Nintendo: the Company, Consoles and Games
San Jose State University SJSU ScholarWorks ART 108: Introduction to Games Studies Art and Art History & Design Departments Fall 12-2020 The History of Nintendo: the Company, Consoles And Games Laurie Takeda San Jose State University Follow this and additional works at: https://scholarworks.sjsu.edu/art108 Part of the Computer Sciences Commons, and the Game Design Commons Recommended Citation Laurie Takeda. "The History of Nintendo: the Company, Consoles And Games" ART 108: Introduction to Games Studies (2020). This Final Class Paper is brought to you for free and open access by the Art and Art History & Design Departments at SJSU ScholarWorks. It has been accepted for inclusion in ART 108: Introduction to Games Studies by an authorized administrator of SJSU ScholarWorks. For more information, please contact [email protected]. The history of Nintendo: the company, consoles and games Introduction A handful of the most popular video games from Mario to The Legend of Zelda, and video game consoles from the Nintendo Entertainment System to the Nintendo Switch, were all created and developed by the same company. That company is Nintendo. From its beginning, Nintendo was not a video gaming company. Since the company’s first launch of the Nintendo Entertainment System, or NES, to the present day of the latest release of the Nintendo Switch from 2017, they have sold over 5 billion video games and over 779 million hardware units globally, according to Nintendo UK (Nintendo UK). As Nintendo continues to release new video games and consoles, they have become one of the top gaming companies, competing alongside Sony and Microsoft. -
New Visions in Citizen Science
case study series vol 3 New Visions in Citizen Science by Anne Bowser and Lea Shanley New Visions in Citizen Science by Anne Bowser and Lea Shanley, Woodrow Wilson Center November 2013 Commons Lab | Case sTUDy series | vOL 3 NEW VISIONS IN CITIZEN SCIENCE Commons Lab Science and Technology Innovation Program Woodrow Wilson International Center for Scholars One Woodrow Wilson Plaza 1300 Pennsylvania Avenue, N.W. Washington, DC 20004-3027 www.CommonsLab.wilsoncenter.org Study Director: Lea Shanley Editor: Aaron Lovell Cover design: Kathy Butterfield and Diana Micheli © 2013, The Woodrow Wilson Center: This work is licensed under Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License: http://creativecommons. org/licenses/by-nc-nd/3.0/ This report may be reproduced in whole, or in part, for educational and non- commercial uses, pursuant to the Creative Commons Attribution-NonCommerical- NoDerivs 3.0 Unported License found at http://creativecommons.org/licenses/by-nc- nd/3.0/ and provided this copyright notice and the following attribution is given: Anne Bowser and Lea Shanley, New Visions in Citizen Science. Washington, DC: Wood- row Wilson International Center for Scholars, 2013. Users may not use technical measures to obstruct or control the reading or further copying of the copies that they make or distribute. Nongovernmental users may not accept compensation of any manner in exchange for copies. The Woodrow Wilson Center is open to certain derivative uses of this product beyond the limitations of the included Creative Commons License, particularly for educational materials targeted at expanding knowledge on the Commons Lab’s mandate. For more information, please contact [email protected].