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Biological information: making it accessible and integrated (and trying to make sense of it)

T. Hubbard
2002 Bioinformatics  
of its diseases.  ...  The availability of the genome sequences of human and mouse, human sequence variation data and other large genetic data sets will lead to a revolution in understanding of the human machine and the treatment  ...  However, it appears that sufficient high quality experimentally curated annotation now exists to be used as a substrate for machine learning algorithms to create effective models of biological signal sequences  ... 
doi:10.1093/bioinformatics/18.suppl_2.s140 pmid:12385995 fatcat:fhimgjeup5gyzoepy2tewrq2cq

Biological Information—Definitions from a Biological Perspective

Jan Charles Biro
2011 Information  
The objective of this paper is to analyze the properties of information in general and to define biological information in particular.  ...  Information is integration of data used to make sense, and knowledge is integration of information to a compact meaning.  ...  A complex sender with access to a large amount of information can create complex messages, and a complex receiver is prepared to make sense of complex messages.  ... 
doi:10.3390/info2010117 fatcat:twvueeyjffg2thuwliafd4d6la

Information in the Biological Sciences [chapter]

Alfredo Marcos, Robert Arp
2013 The Philosophy of Biology  
only in relation to a given cellular context, and it is misguiding to locate information in a particular molecule.  ...  Information has been a central concept for contemporary work in the biological sciences (and other sciences) especially after the publication of Claude Shannon and Warren Weaver's, The Mathematical Theory  ...  In biological terms, we find here the functional aspects of information, its ability to affect the receiver's behavior in a functional or adaptive sense.  ... 
doi:10.1007/978-94-007-6537-5_23 fatcat:idscgqvvenbihbvzcysaexlotm

Biological Systems through the Informational Lens

Albert Lawrence, Tsvi Katchalski, Alex Perez, Varda Lev-Ram, Daniela Boassa, Thomas Deerinck, Sebastien Phan, Steven Peltier, Mark Ellisman
2016 Procedia Computer Science  
In order to deal with fundamental issues related to information processing in biological systems, new data processing methods as well as advances in chemically sensitive probes and imaging technology must  ...  We review how concepts of information and entropy may give new perspectives on the flow of information within biological systems, as well as our instrumentation and computer processing.  ...  It is evident that structural transformations of the chromatin determine when and how DNA can be accessed and read [10, 11, 12] .  ... 
doi:10.1016/j.procs.2016.05.355 fatcat:kf6wtzoje5egnps2npivkhwlfe

Etropy, Information and Evolving Biological Systems

Daniel R. Brooks
2007 Theoria et Historia Scientiarum  
ENTROPY, INFORMATION AND EVOLVING BIOLOGICAL SYSTEMS 1.  ...  Because the production rules are physically encoded in the structure of the system, biological systems are physical information systems, and their expected behavior over time follows a general entropie  ...  Evolution makes sense as an informationally negentropic process only if all genetic possibilities were present at the beginning of life, and we have simply seen a distillation and reduction in those possibilities  ... 
doi:10.12775/ths.1994.004 fatcat:t6qtbdg5wbhtrkcpl6iztoxl24

Experience Using OWL DL for the Exchange of Biological Pathway Information

Alan Ruttenberg, Jonathan Rees, Joanne Luciano
2005 W3C Web Ontology Language (OWL) Experiences and Directions Workshop (OWLED)  
We report on experiences using OWL DL in the design of an exchange format for biological pathway information.  ...  Although the working group charged with this task was not initially very familiar with OWL and knew that the technology around OWL wasn't mature, they chose it because of its ability to express complex  ...  JSL gratefully acknowledges the Office of Biological and Environmental Research Genomics: GTL Program (grant #DE-FG02-04ER63931), George Church, Robert Stevens and the National Science Foundation (grant  ... 
dblp:conf/owled/RuttenbergRL05 fatcat:jsdkymg5prc5hjm2nx2kafoyjy

Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information

Jonathan Wells
2013 Biological Information  
Clearly, the notion of "junk DNA" is obsolete, and the amount of biological information in the genome far exceeds the information in protein-coding regions.  ...  In the 1950s Francis Crick formulated the Central Dogma of molecular biology, which states (in effect) that DNA makes RNA makes protein makes us.  ...  Acknowledgments The author gratefully acknowledges the assistance of Richard v. Sternberg, helpful comments from reviewers, and the financial support of the Discovery Institute.  ... 
doi:10.1142/9789814508728_0009 fatcat:cqojl25q7redvdbjqx3bwgmfya

Causation and Information: Where Is Biological Meaning to Be Found?

Mark Pharoah
2020 Biosemiotics  
AbstractThe term 'information' is used extensively in biology, cognitive science and the philosophy of consciousness in relation to the concepts of 'meaning' and 'causation'.  ...  On this view, and in biological contexts, systems transmit, acquire, assimilate, decode and manipulate it, and in so doing, generate meaning.  ...  Of course, biological meaning comes in many forms. I am not sure how contentious it would be if one were to try to make a tentative list of these forms.  ... 
doi:10.1007/s12304-020-09397-6 fatcat:radxblzcbnh7bbpjnh4hxtw3ra

How Biological Technology Should Inform the Causal Selection Debate

Janella Baxter
2019 Philosophy, Theory, and Practice in Biology  
Work on this project was supported by the Minnesota Center for Philosophy of Science and a grant from the John Templeton Foundation (ID 50191). This paper is dedicated to Elaine Ruth Baxter.  ...  Acknowledgments I would like to thank David Hilbert, Ken Waters, Marcel Weber, Alan Love, and several anonymous reviewers for their invaluable feedback on this article.  ...  Again, this objection mistakes Waters's paradigmatic example of an actual population-namely, a population raised and bred in the laboratory-as the only way to make sense of the actual difference making  ... 
doi:10.3998/ptpbio.16039257.0011.002 fatcat:pm2joao7vvayzhj52rb3k5c4em

Is information a proper observable for biological organization?

G. Longo, P.-A. Miquel, C. Sonnenschein, A.M. Soto
2012 Progress in Biophysics and Molecular Biology  
While the theories of elaboration and transmission of information are valid mathematical theories, their own logic and implicit causal structure make them inimical to biology, and because of it, their  ...  While the theories of elaboration and transmission of information are valid mathematical theories, their own logic and implicit causal structure make them inimical to biology, and because of it, their  ...  We are grateful to Mael Montevil for his critical reading of the manuscript and to Cheryl Schaeberle for her excellent editorial assistance.  ... 
doi:10.1016/j.pbiomolbio.2012.06.004 pmid:22796169 pmcid:PMC3953560 fatcat:rkvu47imo5ef3a4uzxg7yi3ogu

Consciousness as Integrated Information: a Provisional Manifesto

Giulio Tononi
2008 The Biological Bulletin  
The integrated information theory (IIT) starts from phenomenology and makes use of thought experiments to claim that consciousness is integrated information.  ...  Integrated information (⌽) is defined as the amount of information generated by a complex of elements, above and beyond the information generated by its parts.  ...  Acknowledgments I thank David Balduzzi, Chiara Cirelli, and Lice Ghilardi for their help, and the McDonnell Foundation for support. Notes  ... 
doi:10.2307/25470707 pmid:19098144 fatcat:gaqnyml6wbdxlftx36yoxw4bre

Information processing, computation, and cognition

Gualtiero Piccinini, Andrea Scarantino
2010 Journal of biological physics (Print)  
By and large, they serve to make sense of how organisms keep track of their environments and produce behaviors accordingly.  ...  We defend the relevance to cognitive science of both computation, at least in a generic sense, and information processing, in three important senses of the term.  ...  Many psychologists and neuroscientists reject it. If we adopt an all-encompassing notion of computation, we have no way to make sense of this debate.  ... 
doi:10.1007/s10867-010-9195-3 pmid:22210958 pmcid:PMC3006465 fatcat:n37mygozufbhxpicabbcirdxxq

Visual Analysis of Overlapping Biological Networks

David C. Y. Fung, Seok-Hee Hong, Dirk Koschützki, Falk Schreiber, Kai Xu
2009 2009 13th International Conference Information Visualisation  
their usefulness to support biological analysis.  ...  We evaluated our approaches using biological networks including protein interaction network, metabolic network, and gene regulatory network, from the bacterium Escherichia coli and crop plants to demonstrate  ...  It showed that our visualization can support integrated visual analysis of three heterogeneous biological networks (MN, GRN and PIN), and two overlapping metabolic pathways.  ... 
doi:10.1109/iv.2009.55 dblp:conf/iv/FungHKSX09 fatcat:mqywnkobxjcxrfa4x7odumblky

Digital and biological storage systems — a quantitative comparison

Tomasz Bilski
2007 2007 2nd Bio-Inspired Models of Network, Information and Computing Systems  
First we will show some examples of digital-biological systems integration.  ...  Finally, we will try to answer the question: which digital storage systems and media are the best equivalents for brain and DNA storage?  ...  The digital and biological storage systems are already integrated and certainly will be more integrated in the future.  ... 
doi:10.1109/bimnics.2007.4610074 fatcat:xhwcbglt5vbyliop5jbzsqeb7a

bioLogic

Lining Yao, Jifei Ou, Chin-Yi Cheng, Helene Steiner, Wen Wang, Guanyun Wang, Hiroshi Ishii
2015 Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems - CHI '15  
More generally, we try to encourage the research and use of biological responsive materials and interdisciplinary research in HCI.  ...  ABSTRACT Nature has engineered its own actuators, as well as the efficient material composition, geometry and structure to utilize its actuators and achieve functional transformation.  ...  In this paper, we try to demonstrate both the advantages and challenges of our bioactuator for HCI.  ... 
doi:10.1145/2702123.2702611 dblp:conf/chi/YaoOCSWWI15 fatcat:xuj2owspanhxfgmkfzya7atlsi
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