This software note announces a new open-source release of the Maxent software for modeling species distributions from occurrence records and environmental data, and describes a new R package for fitting such models. T...
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This software note announces a new open-source release of the Maxent software for modeling species distributions from occurrence records and environmental data, and describes a new R package for fitting such models. The new release (ver. 3.4.0) will be hosted online by the American Museum of Natural History, along with future versions. It contains small functional changes, most notably use of a complementary log-log (cloglog) transform to produce an estimate of occurrence probability. The cloglog transform derives from the recently-published interpretation of Maxent as an inhomogeneous Poisson process (IPP), giving it a stronger theoretical justification than the logistic transform which it replaces by default. In addition, the new R package, maxnet, fits Maxent models using the glmnet package for regularized generalized linear models. We discuss the implications of the IPP formulation in terms of model inputs and outputs, treating occurrence records as points rather than grid cells and interpreting the exponential Maxent model (raw output) as as an estimate of relative abundance. With these two open-source developments, we invite others to freely use and contribute to the software.
Visual languages (VLs) facilitate softwaredevelopment by not only supporting communication and abstraction, but also by generating various artifacts such as code and reports from the same high-level specification. VL...
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Visual languages (VLs) facilitate softwaredevelopment by not only supporting communication and abstraction, but also by generating various artifacts such as code and reports from the same high-level specification. VLs are thus often translated to other formalisms, in most cases with bidirectionality as a crucial requirement to, e.g., support re-engineering of software systems. Triple Graph Grammars (TGGs) are a rule-based language to specify consistency relations between two (visual) languages from which bidirectional translators are automatically derived. TGGs are formally founded but are also limited in expressiveness, i.e., not all types of consistency can be specified with TGGs. In particular, 1-to-n correspondence between elements depending on concrete input models cannot be described. In other words, a universal quantifier over certain parts of a TGG rule is missing to generalize consistency to arbitrary size. To overcome this, we transfer the well-known multi-amalgamation concept from algebraic graph transformation to TGGs, allowing us to mark certain parts of rules as repeated depending on the translation context. Our main contribution is to derive TGG-based translators that comply with this extension. Furthermore, we identify bad smells on the usage of multi-amalgamation in TGGs, prove that multi-amalgamation increases the expressiveness of TGGs, and evaluate our tool support. (C) 2016 Elsevier Ltd. All rights reserved.
simulation of physiological processes is a powerful tool to help students integrate and apply the knowledge they gained during traditional forms of teaching (e.g., lectures, textbooks). Several physiology simulation p...
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simulation of physiological processes is a powerful tool to help students integrate and apply the knowledge they gained during traditional forms of teaching (e.g., lectures, textbooks). Several physiology simulation packages are commercially available or custom made and are usually tailored to
The authors report on the accomplishments of the "Journal of software: Evolution and Process" in about 5 years since it was born. They also examine and identify new directions for improvement. The journal so...
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The authors report on the accomplishments of the "Journal of software: Evolution and Process" in about 5 years since it was born. They also examine and identify new directions for improvement. The journal sought to address the issues of software conception, development, management, evolution and improvement with a multidisciplinary view.
The authors reflect on issues concerning software usability in computational biology. Topics discussed include a definition of usability, the ten rules for developing usability software, and the importance of usabilit...
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The authors reflect on issues concerning software usability in computational biology. Topics discussed include a definition of usability, the ten rules for developing usability software, and the importance of usability in software design. Also mentioned is the impact of these rules on improving usability of scientific software.
Developing software that scales on multicore processors is an inexact science dominated by guesswork, measurement, and expensive cycles of redesign and reimplementation. Current approaches are workload-driven and, hen...
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Developing software that scales on multicore processors is an inexact science dominated by guesswork, measurement, and expensive cycles of redesign and reimplementation. Current approaches are workload-driven and, hence, can reveal scalability bottlenecks only for known workloads and available software and hardware. This paper introduces an interface-driven approach to building scalable software. This approach is based on the scalable commutativity rule, which, informally stated, says that whenever interface operations commute, they can be implemented in a way that scales. We formalize this rule and prove it correct for any machine on which conflict-free operations scale, such as current cache-coherent multicore machines. The rule also enables a better design process for scalable software: programmers can now reason about scalability from the earliest stages of interface definition through software design, implementation, and evaluation.
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