Semantic Web repositories for genomics data using the eXframe platform

Background: With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. Methods: To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Conclusions: Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge

eXframe: reusable framework for storage, analysis and visualization of genomics experiments

<p>Abstract</p> <p>Background</p> <p>Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types.</p> <p>Results</p> <p>We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients.</p> <p>Conclusion</p> <p>The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications.</p

Increasing Diversity of Faculty and Administrators in the Virginia Community College System

In 2013, Chancellor DuBois convened a Task Force on Diversity with the aim of making the Virginia Community College System (VCCS) a model for diversity by “increasing the demographic diversity of the VCCS so that teaching faculty and leaders look more like the communities we serve” (Chancellors Diversity Task Force, 2014, p. 3). The hard work of the Task Force members culminated in a report that summarized their findings and recommendations, including a “Call to Action” list of 11 steps, many of which have been implemented or are in progress. Several of these key initiatives have put the VCCS on track to meeting its diversity goals: the adoption of a VCCS policy statement on diversity and inclusion; the hiring of a Chief Diversity Officer and appointment of College Diversity representatives at each of the 23 VCCS colleges; the formation of diversity steering committees at each college; and the creation of an online Diversity Dashboard database which provides “institutional and system-wide longitudinal data on gender and minority status” (p. 12). We commend these efforts and would like to build on the foundation provided by the Task Force. Furthermore, we maintain that the success of the Complete 2021: Educating for a Competitive Commonwealth VCCS Strategic Plan depends upon increasing diversity and inclusion across the colleges, particularly in the hiring and retention of more diverse faculty and administrators. Although increasing diversity on college campuses has many benefits, improving student success and completion arguably being the most significant, we believe that campus diversity is intrinsically valuable, apart from the many benefits it affords institutions. This report offers recommendations from the individual to the system level

#IWILLLISTEN

Mental illness affects one in four Americans. In 2012, the National Alliance on Mental Illness (NAMI) in New York City and JWT Ethos created the #IWILLLISTEN campaign to create awareness about this staggering statistic and what people could do to combat the negative stigma associated with mental illness. In 2014, JWT tasked Outlier Advertising to create a campus-focused version of the campaign in the form of an activation plan that could be initiated on any college campus across the nation in the fall of 2014. In addition, JWT asked Outlier Advertising to test elements of the campaign at the University of Nebraska-Lincoln (UNL) campus. They were implemented April 6-16, 2014. The original #IWILLLISTEN campaign focused on soliciting pledges from the general public in the form of short videos and social media status updates, promising to listen to those affected by mental illness. Based on localized market research in Lincoln, Neb., Outlier Advertising determined that an activation plan targeted toward a college community should focus on mental health instead of mental illness when raising awareness and generating pledges. The UNL activation plan included four main events during Greek Week. Pledges were generated on a 15 feet by 3 feet banner that featured the #IWILLLISTEN logo in high-traffic areas around campus. Another event was the University Program Council (UPC) spring concert featuring Big Sean, which was attended by 4,000 people. Blue glow sticks 1 and free water bottles with the #IWILLLISTEN message helped raise awareness while encouraging concert-goers to make a pledge on the banner. At the spring football scrimmage, which was attended by more than 65,000 people, 1,200 blue wristbands featuring the message #IWILLLISTEN were distributed in the student section in addition to the banner being displayed. The final event was a yoga class held at the Recreation Center to give students, faculty and staff an opportunity to relax and promote mental health. All attendees received wristbands and had an opportunity to pledge to listen. All of the events were supported by social media, primarily Twitter and Facebook, using the #IWILLLISTEN hashtag. The social media content included local facts about mental illness at UNL, reminders about upcoming #IWILLLISTEN events, and updates on pledges. One popular tactic was a localized infographic video that was shared by members of the #IWILLLISTEN online community. Outlier Advertising partnered with prominent and like-minded groups on campus to help distribute the message and to create high-quality videos by campus leaders and influencers, including Chancellor Harvey Perlman, Dr. Pat Tetreault, Assistant Director of the LGBTQA+ Resource Center and Charlie Foster, an on-campus licensed healthcare practitioner. At the conclusion of the week, the campaign had reached an audience of over 90,000 in person, 90,000 on social media and received over 550 in-person pledges

GLOBEM Dataset: Multi-Year Datasets for Longitudinal Human Behavior Modeling Generalization

Recent research has demonstrated the capability of behavior signals captured by smartphones and wearables for longitudinal behavior modeling. However, there is a lack of a comprehensive public dataset that serves as an open testbed for fair comparison among algorithms. Moreover, prior studies mainly evaluate algorithms using data from a single population within a short period, without measuring the cross-dataset generalizability of these algorithms. We present the first multi-year passive sensing datasets, containing over 700 user-years and 497 unique users' data collected from mobile and wearable sensors, together with a wide range of well-being metrics. Our datasets can support multiple cross-dataset evaluations of behavior modeling algorithms' generalizability across different users and years. As a starting point, we provide the benchmark results of 18 algorithms on the task of depression detection. Our results indicate that both prior depression detection algorithms and domain generalization techniques show potential but need further research to achieve adequate cross-dataset generalizability. We envision our multi-year datasets can support the ML community in developing generalizable longitudinal behavior modeling algorithms.Comment: Thirty-sixth Conference on Neural Information Processing Systems Datasets and Benchmarks Trac

Toward interoperable bioscience data

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Genetics 44 (2012): 121-126, doi:10.1038/ng.1054.To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.The authors also acknowledge the following funding sources in particular: UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/I000771/1 to S.-A.S. and A.T.; UK BBSRC BB/I025840/1 to S.-A.S.; UK BBSRC BB/I000917/1 to D.F.; EU CarcinoGENOMICS (PL037712) to J.K.; US National Institutes of Health (NIH) 1RC2CA148222-01 to W.H. and the HSCI; US MIRADA LTERS DEB-0717390 and Alfred P. Sloan Foundation (ICoMM) to L.A.-Z.; Swiss Federal Government through the Federal Office of Education and Science (FOES) to L.B. and I.X.; EU Innovative Medicines Initiative (IMI) Open PHACTS 115191 to C.T.E.; US Department of Energy (DOE) DE-AC02- 06CH11357 and Arthur P. Sloan Foundation (2011- 6-05) to J.G.; UK BBSRC SysMO-DB2 BB/I004637/1 and BBG0102181 to C.G.; UK BBSRC BB/I000933/1 to C.S. and J.L.G.; UK MRC UD99999906 to J.L.G.; US NIH R21 MH087336 (National Institute of Mental Health) and R00 GM079953 (National Institute of General Medical Science) to A.L.; NIH U54 HG006097 to J.C. and C.E.S.; Australian government through the National Collaborative Research Infrastructure Strategy (NCRIS); BIRN U24-RR025736 and BioScholar RO1-GM083871 to G.B. and the 2009 Super Science initiative to C.A.S

A high-performance 8 nV/root Hz 8-channel wearable and wireless system for real-time monitoring of bioelectrical signals

Background: It is widely accepted by the scientific community that bioelectrical signals, which can be used for the identification of neurophysiological biomarkers indicative of a diseased or pathological state, could direct patient treatment towards more effective therapeutic strategies. However, the design and realisation of an instrument that can precisely record weak bioelectrical signals in the presence of strong interference stemming from a noisy clinical environment is one of the most difficult challenges associated with the strategy of monitoring bioelectrical signals for diagnostic purposes. Moreover, since patients often have to cope with the problem of limited mobility being connected to bulky and mains-powered instruments, there is a growing demand for small-sized, high-performance and ambulatory biopotential acquisition systems in the Intensive Care Unit (ICU) and in High-dependency wards. Finally, to the best of our knowledge, there are no commercial, small, battery-powered, wearable and wireless recording-only instruments that claim the capability of recording electrocorticographic (ECoG) signals. Methods: To address this problem, we designed and developed a low-noise (8 nV/√Hz), eight-channel, battery-powered, wearable and wireless instrument (55 × 80 mm2). The performance of the realised instrument was assessed by conducting both ex vivo and in vivo experiments. Results: To provide ex vivo proof-of-function, a wide variety of high-quality bioelectrical signal recordings are reported, including electroencephalographic (EEG), electromyographic (EMG), electrocardiographic (ECG), acceleration signals, and muscle fasciculations. Low-noise in vivo recordings of weak local field potentials (LFPs), which were wirelessly acquired in real time using segmented deep brain stimulation (DBS) electrodes implanted in the thalamus of a non-human primate, are also presented. Conclusions: The combination of desirable features and capabilities of this instrument, namely its small size (~one business card), its enhanced recording capabilities, its increased processing capabilities, its manufacturability (since it was designed using discrete off-the-shelf components), the wide bandwidth it offers (0.5 – 500 Hz) and the plurality of bioelectrical signals it can precisely record, render it a versatile and reliable tool to be utilized in a wide range of applications and environments

The biology of color

Coloration mediates the relationship between an organism and its environment in important ways, including social signaling, antipredator defenses, parasitic exploitation, thermoregulation, and protection from ultraviolet light, microbes, and abrasion. Methodological breakthroughs are accelerating knowledge of the processes underlying both the production of animal coloration and its perception, experiments are advancing understanding of mechanism and function, and measurements of color collected noninvasively and at a global scale are opening windows to evolutionary dynamics more generally. Here we provide a roadmap of these advances and identify hitherto unrecognized challenges for this multi- and interdisciplinary field