COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Analysis and Synthesis of Metadata Goals for Scientific Data

The proliferation of discipline-specific metadata schemes contributes to artificial barriers that can impede interdisciplinary and transdisciplinary research. The authors considered this problem by examining the domains, objectives, and architectures of nine metadata schemes used to document scientific data in the physical, life, and social sciences. They used a mixed-methods content analysis and Greenberg’s (2005) metadata objectives, principles, domains, and architectural layout (MODAL) framework, and derived 22 metadata-related goals from textual content describing each metadata scheme. Relationships are identified between the domains (e.g., scientific discipline and type of data) and the categories of scheme objectives. For each strong correlation (\u3e0.6), a Fisher’s exact test for nonparametric data was used to determine significance (p \u3c .05). Significant relationships were found between the domains and objectives of the schemes. Schemes describing observational data are more likely to have “scheme harmonization” (compatibility and interoperability with related schemes) as an objective; schemes with the objective “abstraction” (a conceptual model exists separate from the technical implementation) also have the objective “sufficiency” (the scheme defines a minimal amount of information to meet the needs of the community); and schemes with the objective “data publication” do not have the objective “element refinement.” The analysis indicates that many metadata-driven goals expressed by communities are independent of scientific discipline or the type of data, although they are constrained by historical community practices and workflows as well as the technological environment at the time of scheme creation. The analysis reveals 11 fundamental metadata goals for metadata documenting scientific data in support of sharing research data across disciplines and domains. The authors report these results and highlight the need for more metadata-related research, particularly in the context of recent funding agency policy changes

Constant rate thermal analysis for thermal stability studies of polymers

This paper explores the relationship between the shapes of temperature-time curves obtained from experimental data recorded by means of constant rate thermal analysis (CRTA) and the kinetic model followed by the thermal degradation reaction. A detailed shape analysis of CRTA curves has been performed as a function of the most common kinetic models. The analysis has been validated with simulated data, and with experimental data recorded from the thermal degradation of polytetrafluoroethylene (PTFE), poly(1,4-butylene terephthalate) (PBT), polyethylene (PE) and poly(vinyl chloride) (PVC). The resulting temperature-time profiles indicate that the studied polymers decompose through phase boundary, random scission, diffusion and nucleation mechanisms respectively. The results here presented demonstrate that the strong dependence of the temperature-time profile on the reaction mechanism would allow the real kinetic model obeyed by a reaction to be discerned from a single CRTA curve.Junta de Andalucía TEP-03002Ministerio de Ciencia e Innovación MAT 2008-06619/MA

Requirements for Topology in 3D GIS

Topology and its various benefits are well understood within the context of 2D Geographical Information Systems. However, requirements in three-dimensional (3D) applications have yet to be defined, with factors such as lack of users' familiarity with the potential of such systems impeding this process. In this paper, we identify and review a number of requirements for topology in 3D applications. The review utilises existing topological frameworks and data models as a starting point. Three key areas were studied for the purposes of requirements identification, namely existing 2D topological systems, requirements for visualisation in 3D and requirements for 3D analysis supported by topology. This was followed by analysis of application areas such as earth sciences and urban modelling which are traditionally associated with GIS, as well as others including medical, biological and chemical science. Requirements for topological functionality in 3D were then grouped and categorised. The paper concludes by suggesting that these requirements can be used as a basis for the implementation of topology in 3D. It is the aim of this review to serve as a focus for further discussion and identification of additional applications that would benefit from 3D topology. © 2006 The Authors. Journal compilation © 2006 Blackwell Publishing Ltd

How Courts Adjudicate Patent Definiteness and Disclosure

Section 112 of the Patent Act requires patentees to clearly explain what their invention is (a requirement known as claim definiteness), as well as how to make and use it (the disclosure requirements of enablement and written description). Many concerns about the modern patent system stem from these requirements. But despite the critical importance of § 112 to the functioning of the patent system, there is surprisingly little empirical data about how it has been applied in practice. To remedy the reliance on anecdotes, we have created a hand-coded dataset of 1144 reported court decisions from 1982 to 2012 in which U.S. district courts or the Court of Appeals for the Federal Circuit rendered a decision on the enablement, written-description, or claim-definiteness requirements of § 112. We coded validity outcomes under these three doctrines on a novel five-level scale so as to capture significant subtlety in the strength of each decision, and we also classified patents by technology and industry categories. We also coded for a number of litigation characteristics that could arguably influence outcomes. Although one must be cautious about generalizing from reported decisions due to selection effects, our results show some statistically significant disparities in § 112 outcomes for different technologies and industries—although fewer than the conventional wisdom suggests, and not always in the direction that many have believed. Just as importantly, our analysis reveals significant relationships between other variables and § 112 litigation outcomes, including whether a district court or the Federal Circuit made the last decision in a case, whether a patent claim was drafted in means-plus-function format, and whether a case was decided before or after Markman v. Westview Instruments. Our results showing how § 112 has been applied in practice will be helpful in evaluating current proposals for reform, and our rich dataset will enable more systematic studies of these critical doctrines in the future

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure