1,150 research outputs found
Short Courses: Flexible Learning Opportunities in Informatics
In today’s fast-paced, data-driven world, researchers need to have a good foundation in informatics to store, organize, process, and analyze growing amounts of data. However, not all degree programs offer such training. Obtaining training in informatics on your own can be a daunting task for both new and established researchers who have little informatics experience. Providing educational opportunities appropriate for various skill levels and that mesh with a full-time schedule can remove barriers and foster a collaborative, informatics-savvy community that is better equipped to push science forward.
To enhance informatics education in bioinformatics, VCUs Wright Center for Clinical and Translational Research of- fers a complementary series of seminars and workshops. These short course offerings introduce attendees to bioinformatics concepts and applications, and provide hands-on experience using online Bioinformatics databases. Bioinformatics 101 (B101) is an 8-week long series of 1-hour seminars focused on introducing topics in bioinformatics related to Next Generation Sequencing (NGS). Lectures are application focused and include overviews of NGS technology, practical bioinformatics pipelines, and examples of how the technology can influence downstream bioinformatics analyses. Bioinformatics 102 (B102) is a 5-day, 2 hours per day workshop developed in collaboration with VCU Libraries that provides attendees with hands-on experience accessing and using public data repositories. Sessions include a brief lecture followed by hands-on exercises. A Certificate of Completion is awarded upon meeting certain criteria for either the 101 or 102 courses.
Bioinformatics 101 has been offered 3 times with a combined total of 246 registrants, and Bioinformatics 102 has been offered twice with a total of 78 registrants (limited to 30 per session per day). From course surveys, 82% (n=108) and 95% (n=47) of respondents gave B101 and B102 a positive rating, respectively. In addition, 89% of B101 respondents indicated their knowledge was improved, with 100% of B102 respondents indicating the same. A total of 84 and 33 certificates have been awarded for B101 and B102, respectively.
The Bioinformatics 101 and 102 courses have become highly anticipated across the university, and have gained the external attention of surrounding businesses and colleges. Registrants have diverse backgrounds including biological, clinical, computational, administrative, librarian, business, and others with a total of 77 departments across VCU and VCU Health represented. Due to this interest, Bioinformatics 101 began offering live online attendance to accommodate those who were unable to travel across campus, or who are attending from outside VCU. This past year, 50% of attendance was online indicating a growing need for flexible education opportunities in informatics.
Increasing researcher knowledge of Bioinformatics along with awareness of university resources for informatics support fosters an informatics-savvy research community that is empowered to take advantage of existing and new data sources in the pursuit of new insights and scientific discoveries for the betterment of human health. Future work will include the development of a more comprehensive educational framework by creating new and flexible learning opportunities that will make informatics education easy and convenient for our dedicated researchers
Providing Hands-on Training with Bioinformatics Databases: A Collaboration Between VCU Libraries & Wright Center for Clinical and Translational Research
BackgroundWith the goal of increasing specialized services for researchers, Virginia Commonwealth University (VCU) Libraries sent its basic science librarians to an intensive training on bioinformatics databases, “A Librarian’s Guide to NCBI.” VCU’s Wright Center for Clinical and Translational Research (Wright CCTR) was expanding the educational component of its bioinformatics support around the same time. This year, the librarians partnered with the Wright CCTR to offer an introductory bioinformatics database workshop introducing researchers to genetic/genomic databases. MethodsFor one week in June, sessions were conducted introducing up to 30 faculty and staff to The Cancer Genome Atlas and NCBI’s Gene, BLAST, Variation Viewer and Gene Expression Omnibus. Librarians taught resources they learned in the NCBI training, and Wright CCTR staff taught resources they use often. Each day’s 1.5 hour session included presentations, demonstrations, and hands-on assignment time. Certificates were awarded to participants who completed 4 out of 5 assignments. ResultsRegistration for the workshop was full in under a week with a waiting list. All survey respondents (n=27) evaluated the overall quality of the workshop as good or excellent and indicated that they would recommend the workshop to a colleague or student. ConclusionsThis successful partnership between VCU Libraries and the Wright CCTR allowed for a broader range of bioinformatics topics to be covered, in addition to easing the planning and teaching workload for each group. The strong interest in this series across a variety of disciplines from both VCU and VCU Health indicates a need for staff and faculty-oriented bioinformatics training within the university
Phenotypic indicators to identify methionine rich European grain legumes and the correlation of grain methionine contents with the sulphur supply
Home grown legumes are a valuable protein source for pure on-farm diets for livestock in organic farming. Whereas protein of Glycine max naturally has higher contents of methionine nand also lysine typical European grain legumes (Pisum sativum L., Vicia faba L., Lupinus angustifolius L.) used in organic farms as component of animal food are relatively low in those amino acids
Templeting of Thin Films Induced by Dewetting on Patterned Surfaces
The instability, dynamics and morphological transitions of patterns in thin
liquid films on periodic striped surfaces (consisting of alternating less and
more wettable stripes) are investigated based on 3-D nonlinear simulations that
account for the inter-site hydrodynamic and surface-energetic interactions. The
film breakup is suppressed on some potentially destabilizing nonwettable sites
when their spacing is below a characteristic lengthscale of the instability,
the upper bound for which is close to the spinodal lengthscale. The thin film
pattern replicates the substrate surface energy pattern closely only when, (a)
the periodicity of substrate pattern matches closely with the characteristic
lengthscale, and (b) the stripe-width is within a range bounded by a lower
critical length, below which no heterogeneous rupture occurs, and an upper
transition length above which complex morphological features bearing little
resemblance to the substrate pattern are formed.Comment: 5 pages TeX (REVTeX 4), other comments: submitted to Phys. Rev.Let
Wurtzite Effects on Spin Splitting of GaN/AlN Quantum Wells
A new mechanism (DeltaC1-DeltaC3 coupling) is accounted for the spin
splitting of wurtzite GaN, which is originated from the intrinsic wurtzite
effects (band folding and structure inversion asymmetry). The band-folding
effect generates two conduction bands (DeltaC1 and DeltaC3), in which p-wave
probability has tremendous change when kz approaches anti-crossing zone. The
spin-splitting energy induced by the DeltaC1-DeltaC3 coupling and wurtzite
structure inversion asymmetry is much larger than that evaluated by traditional
Rashba or Dresselhaus effects. When we apply the coupling to GaN/AlN quantum
wells, we find that the spin-splitting energy is sensitively controllable by an
electric field. Based on the mechanism, we proposed a p-wave-enhanced
spin-polarized field effect transistor, made of InxGa1-xN/InyAl1-yN, for
spintronics application.Comment: 12 pages, 4 figures (total 16 pages
Geometry dominated fluid adsorption on sculptured substrates
Experimental methods allow the shape and chemical composition of solid
surfaces to be controlled at a mesoscopic level. Exposing such structured
substrates to a gas close to coexistence with its liquid can produce quite
distinct adsorption characteristics compared to that occuring for planar
systems, which may well play an important role in developing technologies such
as super-repellent surfaces or micro-fluidics. Recent studies have concentrated
on adsorption of liquids at rough and heterogeneous substrates and the
characterisation of nanoscopic liquid films. However, the fundamental effect of
geometry has hardly been addressed. Here we show that varying the shape of the
substrate can exert a profound influence on the adsorption isotherms allowing
us to smoothly connect wetting and capillary condensation through a number of
novel and distinct examples of fluid interfacial phenomena. This opens the
possibility of tailoring the adsorption properties of solid substrates by
sculpturing their surface shape.Comment: 6 pages, 4 figure
Indirekte Selektionmethoden auf Methioninreichtum des Samenproteins bei heimischen Leguminosen
While grain legumes can be regarded as highly valuable protein sources for animal nutrition, ceratin drawbacks inhibit their use as sole foodstuff for livestock. The nutrient quality is reduced by low concentrations of tryptophan and sulfur amino acids
Dewetting of thin films on heterogeneous substrates: Pinning vs. coarsening
We study a model for a thin liquid film dewetting from a periodic
heterogeneous substrate (template). The amplitude and periodicity of a striped
template heterogeneity necessary to obtain a stable periodic stripe pattern,
i.e. pinning, are computed. This requires a stabilization of the longitudinal
and transversal modes driving the typical coarsening dynamics during dewetting
of a thin film on a homogeneous substrate. If the heterogeneity has a larger
spatial period than the critical dewetting mode, weak heterogeneities are
sufficient for pinning. A large region of coexistence between coarsening
dynamics and pinning is found.Comment: 4 pages, 4 figure
Macroscopic transport by synthetic molecular machines
Nature uses molecular motors and machines in virtually every significant biological process, but demonstrating that simpler artificial structures operating through the same gross mechanisms can be interfaced with—and perform physical tasks in—the macroscopic world represents a significant hurdle for molecular nanotechnology. Here we describe a wholly synthetic molecular system that converts an external energy source (light) into biased brownian motion to transport a macroscopic cargo and do measurable work. The millimetre-scale directional transport of a liquid on a surface is achieved by using the biased brownian motion of stimuli-responsive rotaxanes (‘molecular shuttles’) to expose or conceal fluoroalkane residues and thereby modify surface tension. The collective operation of a monolayer of the molecular shuttles is sufficient to power the movement of a microlitre droplet of diiodomethane up a twelve-degree incline.
Anomalous k-dependent spin splitting in wurtzite AlxGa1-xN/GaN heterostructures
We have confirmed the k-dependent spin splitting in wurtzite AlxGa1-xN/GaN
heterostructures. Anomalous beating pattern in Shubnikov-de Haas measurements
arises from the interference of Rashba and Dresselhaus spin-orbit interactions.
The dominant mechanism for the k-dependent spin splitting at high values of k
is attributed to Dresselhaus term which is enhanced by the Delta C1-Delta C3
coupling of wurtzite band folding effect
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