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Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections:•Reviews of Computational Methods•Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels•The Interface of Biotic and Abiotic Processes•Processing of Large Data Sets for Enhanced Analysis•Parameter Optimization and Measurement
n/a --- inosine --- immune checkpoint inhibitor --- geometric singular perturbation theory --- simulation --- BioModels Database --- ADAR --- calcium current --- bifurcation analysis --- bacterial biofilms --- nonlinear dynamics --- explanatory model --- turning point bifurcation --- oscillator --- workflow --- bioreactor integrated modeling --- modeling methods --- elementary flux modes visualization --- multiscale systems biology --- evolutionary algorithm --- metabolic model --- differential evolution --- reduced-order model --- computational model --- gut microbiota dysbiosis --- canard-induced EADs --- computational biology --- metabolic modelling --- methods --- SREBP-2 --- mechanistic model --- systems modeling --- biological networks --- macromolecular composition --- provenance --- flux balance analysis --- immunotherapy --- compartmental modeling --- immuno-oncology --- metabolic network visualization --- mechanism --- bistable switch --- Clostridium difficile infection --- bioreactor operation optimization --- microRNA targeting --- CFD simulation --- biomass reaction --- RNA editing --- ordinary differential equation --- metabolic modeling --- mass-action networks --- hybrid model --- multiple time scales --- quantitative systems pharmacology (QSP) --- mathematical modeling --- microRNA --- cancer --- parameter optimization --- Hopf bifurcation --- breast
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Modern information communication technology eradicates barriers of geographic distances, making the world globally interdependent, but this spatial globalization has not eliminated cultural fragmentation. The Two Cultures of C.P. Snow (that of science–technology and that of humanities) are drifting apart even faster than before, and they themselves crumble into increasingly specialized domains. Disintegrated knowledge has become subservient to the competition in technological and economic race leading in the direction chosen not by the reason, intellect, and shared value-based judgement, but rather by the whims of autocratic leaders or fashion controlled by marketers for the purposes of political or economic dominance. If we want to restore the authority of our best available knowledge and democratic values in guiding humanity, first we have to reintegrate scattered domains of human knowledge and values and offer an evolving and diverse vision of common reality unified by sound methodology. This collection of articles responds to the call from the journal Philosophies to build a new, networked world of knowledge with domain specialists from different disciplines interacting and connecting with other knowledge-and-values-producing and knowledge-and-values-consuming communities in an inclusive, extended, contemporary natural–philosophic manner. In this process of synthesis, scientific and philosophical investigations enrich each other—with sciences informing philosophies about the best current knowledge of the world, both natural and human-made—while philosophies scrutinize the ontological, epistemological, and methodological foundations of sciences, providing scientists with questions and conceptual analyses. This is all directed at extending and deepening our existing comprehension of the world, including ourselves, both as humans and as societies, and humankind.
pessimistic induction --- n/a --- qualitative ontology --- dissipative structures --- physicalism --- agent-based reasoning --- thermodynamics --- the logic of nature --- reverse mathematics --- theoretical unity --- state-space approach --- common good --- naturalization of logic --- monad --- metaphysics --- reflexive psychology --- knowledge --- neurodynamics --- consciousness --- third-way reasoning --- induction and discovery of laws --- mind-matter relations --- exoplanet --- Second Law of thermodynamics --- unitarity --- philosophical foundations --- in the name of nature --- big crunch --- epistemology --- eco-cognitive model --- active imagination --- aesthetics in science --- science --- second-person description --- subsumptive hierarchy --- 1st-person and 3rd-person perspectives --- discursive space --- space flight --- complexity --- cybernetics --- cosmology --- matter --- realism --- eco-cognitive openness --- hylomorphism --- measurement --- fallacies --- induction --- vacuum --- physics --- mental representation --- embodiment --- problem of induction --- contradiction --- internalism --- Jungian psychology --- synthesis --- exceptional experiences --- mind --- relational biology --- symmetry breaking --- emergence --- phenomenological psychology --- Aristotle’s four causes --- humanistic management --- real computing --- A.N. Whitehead --- final cause --- naturalism --- induction and concept formation --- temporality --- dispositions --- dark energy --- heterogeneity --- Naturphilosophie --- computation --- causality --- memory evolutive system --- natural philosophy --- quantum computing --- philosophy of information --- self --- information --- analytical psychology --- logic --- indeterminacy --- scientific method --- dialectics --- computability --- language --- ethics --- perception --- philosophy of nature --- agonism --- errors of reasoning --- everyday lifeworld --- emptiness --- awareness --- unity of knowledge --- digitization --- fitness --- depth psychology --- info-computational model --- creativity --- ontology --- philosophy as a way of life --- development --- void --- big freeze --- signal transduction --- abduction --- retrocausality --- dual-aspect monism --- quantum information --- theoretical biology --- acategoriality --- epistemic norms --- evolutionary psychology --- apophasis --- differentiation --- memory --- centripetality --- mathematics --- Leibniz --- Ivor Leclerc --- spatial representation --- subjective experience --- intentionality --- evidence and justification --- internal quantum state --- scientific progress --- holographic encoding --- information-theory --- qualia --- anticipation --- naturalization --- F.W.J. Schelling --- L. Smolin --- R.M. Unger --- Aristotle --- dual aspects --- process --- theory of everything --- philosophy of science --- cognition --- compositional hierarchy --- autocatalysis --- discourse --- emergentist reductionism --- form --- regulation --- contingency --- endogenous selection --- category theory --- Science --- Philosophy of nature. --- Philosophy. --- Nature --- Nature, Philosophy of --- Natural theology --- Normal science --- Philosophy of science --- Philosophy --- Aristotle's four causes
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