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Concept: Application programming interface


The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data.

Concepts: Computer program, Database, Application software, Graphical user interface, Application programming interface, C, Bioinformatics, Computer software


Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1-2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility.

Concepts: How to Solve It, Optimization, Mathematical model, Computer program, Computer simulation, Operations research, Optimal control, Application programming interface


Develop and test web services to retrieve and identify the most precise ICD-10-CM code(s) for a given clinical encounter. Facilitate creation of user interfaces that 1) provide an initial shortlist of candidate codes, ideally visible on a single screen; and 2) enable code refinement.

Concepts: Application programming interface, Source code, Systematized Nomenclature of Medicine, User interface, SNOMED CT, Code, Clinical Data Interchange Standards Consortium, Java


We present a formulation of 4-component relativistic self-consistent field (SCF) theory for a molecular solute described within the framework of the polarizable continuum model (PCM) for solvation. The linear response function for a 4-component PCM-SCF state is also derived. The explicit form of the additional contributions to the first-order response equations is given. The implementation of such a 4-component PCM-SCF model, as carried out in a development version of the DIRAC program package, is documented. In particular, we present the newly developed application programming interface (API) PCMSolver used in the actual implementation with DIRAC. To demonstrate the applicability of the approach we present and analyze calculations of solvation effects on the geometries, electric dipole moments and static electric dipole polarizabilities for the Group 16 Dihydrides H2X (X = O, S, Se, Te, Po).

Concepts: Model theory, Electric dipole moment, Dirac delta function, Polarizable continuum model, Interface, Dipole, Fundamental physics concepts, Application programming interface


The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10-15 years. At the same time, new technologies and the electronic health record (EHR) in particular have permeated the oncology clinic. Initially designed as billing and clinical documentation systems, EHR systems have not anticipated the complexity and variety of genomic information that needs to be reviewed, interpreted, and acted upon on a daily basis. Improved integration of cancer genomic data with EHR systems will help guide clinician decision making, support secondary uses, and ultimately improve patient care within oncology clinics. Some of the key factors relating to the challenge of integrating cancer genomic data into EHRs include: the bioinformatics pipelines that translate raw genomic data into meaningful, actionable results; the role of human curation in the interpretation of variant calls; and the need for consistent standards with regard to genomic and clinical data. Several emerging paradigms for integration are discussed in this review, including: non-standardized efforts between individual institutions and genomic testing laboratories; “middleware” products that portray genomic information, albeit outside of the clinical workflow; and application programming interfaces that have the potential to work within clinical workflow. The critical need for clinical-genomic knowledge bases, which can be independent or integrated into the aforementioned solutions, is also discussed.

Concepts: Clinic, Health informatics, Electronic medical record, Health care, Medicine, Application programming interface, Personal health record, Electronic health record


The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database ( This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.

Concepts: Chemistry, Computer program, Learning, User interface, Algorithm, Interface, Application programming interface, Machine learning


Dynamic social media content, such as Twitter messages, can be used to examine individuals' beliefs and perceptions. By analyzing Twitter messages, this study examines how Twitter users exchanged and recognized toponyms (city names) for different cities in the United States. The frequency and variety of city names found in their online conversations were used to identify the unique spatiotemporal patterns of “geographical awareness” for Twitter users. A new analytic method, Knowledge Discovery in Cyberspace for Geographical Awareness (KDCGA), is introduced to help identify the dynamic spatiotemporal patterns of geographic awareness among social media conversations. Twitter data were collected across 50 U.S. cities. Thousands of city names around the world were extracted from a large volume of Twitter messages (over 5 million tweets) by using the Twitter Application Programming Interface (APIs) and Python language computer programs. The percentages of distant city names (cities located in distant states or other countries far away from the locations of Twitter users) were used to estimate the level of global geographical awareness for Twitter users in each U.S. city. A Global awareness index (GAI) was developed to quantify the level of geographical awareness of Twitter users from within the same city. Our findings are that: (1) the level of geographical awareness varies depending on when and where Twitter messages are posted, yet Twitter users from big cities are more aware of the names of international cities or distant US cities than users from mid-size cities; (2) Twitter users have an increased awareness of other city names far away from their home city during holiday seasons; and (3) Twitter users are more aware of nearby city names than distant city names, and more aware of big city names rather than small city names.

Concepts: Houston, Global city, Application programming interface, Chicago, Los Angeles, Twitter, United States, City


The second meeting of the International Collaboration for Automation of Systematic Reviews (ICASR) was held 3-4 October 2016 in Philadelphia, Pennsylvania, USA. ICASR is an interdisciplinary group whose aim is to maximize the use of technology for conducting rapid, accurate, and efficient systematic reviews of scientific evidence. Having automated tools for systematic review should enable more transparent and timely review, maximizing the potential for identifying and translating research findings to practical application. The meeting brought together multiple stakeholder groups including users of summarized research, methodologists who explore production processes and systematic review quality, and technologists such as software developers, statisticians, and vendors. This diversity of participants was intended to ensure effective communication with numerous stakeholders about progress toward automation of systematic reviews and stimulate discussion about potential solutions to identified challenges. The meeting highlighted challenges, both simple and complex, and raised awareness among participants about ongoing efforts by various stakeholders. An outcome of this forum was to identify several short-term projects that participants felt would advance the automation of tasks in the systematic review workflow including (1) fostering better understanding about available tools, (2) developing validated datasets for testing new tools, (3) determining a standard method to facilitate interoperability of tools such as through an application programming interface or API, and (4) establishing criteria to evaluate the quality of tools' output. ICASR 2016 provided a beneficial forum to foster focused discussion about tool development and resources and reconfirm ICASR members' commitment toward systematic reviews' automation.

Concepts: 2016, Systematic review, Time, Interface, Peer review, Computer program, Stakeholder, Application programming interface


The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.

Concepts: Protein Data Bank, Protein structure, DNA, Genetics, Gene, Genomics, Application programming interface, Scientific method


Brain-Computer Interface (BCI) is a set of technologies that are of increasing interest to researchers. BCI has been proposed as assistive technology for individuals who are non-communicative or paralyzed, such as those with amyotrophic lateral sclerosis or spinal cord injury. The technology has also been suggested for enhancement and entertainment uses, and there are companies currently marketing BCI devices for those purposes (e.g., gaming) as well as health-related purposes (e.g., communication). The unprecedented direct connection created by BCI between human brains and computer hardware raises various ethical, social, and legal challenges that merit further examination and discussion.

Concepts: Innovation, Central nervous system, Application programming interface, Neuron, Spinal cord, Human brain, Brain, Amyotrophic lateral sclerosis