WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further

Boundary quantum critical phenomena with entanglement renormalization

We extend the formalism of entanglement renormalization to the study of boundary critical phenomena. The multi-scale entanglement renormalization ansatz (MERA), in its scale invariant version, offers a very compact approximation to quantum critical ground states. Here we show that, by adding a boundary to the scale invariant MERA, an accurate approximation to the critical ground state of an infinite chain with a boundary is obtained, from which one can extract boundary scaling operators and their scaling dimensions. Our construction, valid for arbitrary critical systems, produces an effective chain with explicit separation of energy scales that relates to Wilson's RG formulation of the Kondo problem. We test the approach by studying the quantum critical Ising model with free and fixed boundary conditions.Comment: 8 pages, 12 figures, for a related work see arXiv:0912.289

BridgeDb: standardized access to gene, protein and metabolite identifier mapping services

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

The BridgeDb library is available at "http://www.bridgedb.org":http://www.bridgedb.org.
A paper about BridgeDb was published in BMC _Bioinformatics_, 2010 Jan 4;11(1):5.

BridgeDb blog: "http://www.helixsoft.nl/blog/?tag=bridgedb":http://www.helixsoft.nl/blog/?tag=bridged

Autonomy, Good Humor and Support Networks, Potential of Community Resilience Intervention in People Victims of the Earthquake in the Calderón Parish

Resilience is a concept widely used in recent years, especially when it comes to evaluating the level of recovery of communities that are hit by natural phenomena. It can be stated that conceptually resilience constitutes the ability to react effectively and quickly to the effects of disasters, being a complex phenomenon to evaluate and define. And although the level of resilience does not necessarily imply greater control of vulnerability, it can be affirmed that the reduction of vulnerable conditions can strengthen and consolidate the resilient capacity of individuals and communities, in the face of the effects of natural disasters

Dendritic Spine Morphology Determines Membrane-Associated Protein Exchange between Dendritic Shafts and Spine Heads

The purpose of this study was to examine whether variability in the shape of dendritic spines affects protein movement within the plasma membrane. Using a combination of confocal microscopy and the fluorescence loss in photobleaching technique in living hippocampal CA1 pyramidal neurons expressing membrane-linked GFP, we observed a clear correlation between spine shape parameters and the diffusion and compartmentalization of membrane-associated proteins. The kinetics of membrane-linked GFP exchange between the dendritic shaft and the spine head compartment were slower in dendritic spines with long necks and/or large heads than in those with short necks and/or small heads. Furthermore, when the spine area was reduced by eliciting epileptiform activity, the kinetics of protein exchange between the spine compartments exhibited a concomitant decrease. As synaptic plasticity is considered to involve the dynamic flux by lateral diffusion of membrane-bound proteins into and out of the synapse, our data suggest that spine shape represents an important parameter in the susceptibility of synapses to undergo plastic chang

RCK Domain Model of Calcium Activation in BK Channels

Potassium ion channels are ubiquitously expressed from bacteria to mammals where they are involved in various processes ranging from the regulation of osmotic pressure in a single cell to the electrical response in muscle fibers to the generation of action potentials in neurons. The B K channel family (BK for Big K+ conductance) is an interesting subfamily of K+ channels responsive to both membrane voltage and intracellular calcium ion. The unique, high-affinity Ca2+ sensitivity of B K channels is critical to their physiological function in various cell types. The mechanism by which Ca2+ activates B K channel gating, however, is not well understood. Here we present a structure-based approach to the study of B K channels with the goal of providing a structural and functional model of the Ca2+-activation mechanism. Sequence analysis of BK channel C-terminal domains and domains from prokaryotic homologs reveals the conservation of unique positions defining a novel regulatory domain associated with K conduction, the R C K domain. Crystal structures of R C K domains from prokaryotic sources relate the conservation of sequence to the structure, assembly and function of these domains. W e propose a hypothetical model for the structure and function of the Cterminal domains of B K as a set of R C K domains that conduct the Ca -activation mechanism. The features and constraints predicted by the R C K domain model are tested by the electrophysiological assay of a variety of human B K constructs. The results support a domain structure and assembly consistent with the proposed model for the B K C-terminus. In addition, the results identify residues and regions involved in Ca + activation: the Ca2+-binding event and the transduction of the binding energy through protein conformational changes to the channel domain. The R C K domain model thus provides a framework for the study of Ca2+ activation in B K channels

GenMAPP 2: New features and resources for pathway analysis

BACKGROUND: Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses. RESULTS: To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. CONCLUSION: GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms

On the Use of Finite-Size Scaling to Measure Spin-Glass Exponents

Finite-size scaling (FSS) is a standard technique for measuring scaling exponents in spin glasses. Here we present a critique of this approach, emphasizing the need for all length scales to be large compared to microscopic scales. In particular we show that the replacement, in FSS analyses, of the correlation length by its asymptotic scaling form can lead to apparently good scaling collapses with the wrong values of the scaling exponents.Comment: RevTeX, 5 page

Entanglement renormalization and boundary critical phenomena

The multiscale entanglement renormalization ansatz is applied to the study of boundary critical phenomena. We compute averages of local operators as a function of the distance from the boundary and the surface contribution to the ground state energy. Furthermore, assuming a uniform tensor structure, we show that the multiscale entanglement renormalization ansatz implies an exact relation between bulk and boundary critical exponents known to exist for boundary critical systems.Comment: 6 pages, 4 figures; for a related work see arXiv:0912.164

The Scrounge-atron: a phased approach to the Advanced Hydrotest Facility utilizing proton radiography

The Department of Energy has initiated its Stockpile Stewardship and Management Program (SSMP) to provide a single, integrated technical program for maintaining the continued safety and reliability of the nation's nuclear weapons stockpile in the absence of nuclear testing. Consistent with the SSMP, the Advanced Hydrotest Facility (AHF) has been conceived to provide improved radiographic imaging with multiple axes and multiple time frames. The AHF would be used to better understand the evolution of nuclear weapon primary implosion shape under normal and accident scenarios. There are three fundamental technologies currently under consideration for use on the AHF. These include linear induction acceleration, inductive-adder pulsed-power technology (both technologies using high current electron beams to produce an intense X-ray beam) and high-energy proton accelerators to produce a proton beam. The Scrounge-atron (a proton synchrotron) was conceived to be a relatively low cost demonstration of the viability of the third technology using bursts of energetic protons, magnetic lenses, and particle detectors to produce the radiographic image. In order for the Scrounge-atron to provide information useful for the AHF technology decision, the accelerator would have to be built as quickly and as economically as possible. These conditions can be met by "scrounging" parts from decommissioned accelerators across the country, especially the Main Ring at Fermilab. The Scrounge-atron is designed to meet the baseline parameters for single axis proton radiography: a 20 GeV proton beam of ten pulses, 10 degrees protons each, spaced 250 ns apart. (2 refs)