There are two input data processors that are regulatory components of the AERMOD modeling system: AERMET, a meteorological data preprocessor that incorporates air dispersion based on planetary boundary layer turbulence structure and scaling concepts, and AERMAP, a terrain data preprocessor that incorporates complex terrain using USGS Digital Elevation Data. Other non-regulatory components of this system include: AERSCREEN, a screening version of AERMOD; AERSURFACE, a surface characteristics preprocessor, and BPIPPRIM, a multi-building dimensions program incorporating the GEP technical procedures for PRIME applications.
Abstract:The identification of nearly all proteins in a biological system using data-dependent acquisition (DDA) tandem mass spectrometry has become routine for organisms with relatively small genomes such as bacteria and yeast. Still, the quantification of the identified proteins may be a complex process and often requires multiple different software packages. In this protocol, I describe a flexible strategy for the identification and label-free quantification of proteins from bottom-up proteomics experiments. This method can be used to quantify all the detectable proteins in any DDA dataset collected with high-resolution precursor scans and may be used to quantify proteome remodeling in response to drug treatment or a gene knockout. Notably, the method is statistically rigorous, uses the latest and fastest freely-available software, and the entire protocol can be completed in a few hours with a small number of data files from the analysis of yeast.Keywords: shotgun proteomics; mass spectrometry; protein quantification; peptide quantification; data-dependent acquisition
ADMS-1H Advanced Data Management System For The VX-2 64 Bit
We note that PhysiCell can manually implement molecular-scale biology as ODEs (e.g., as in the drug damage example) via custom functions and data, but this is currently difficult to scale to large systems of ODEs with many parameters. Moreover, while we have provided examples of user-defined cell cycle models and other custom functions in the User Guide, sample codes, and tutorials, we do not provide templates for such functions beyond the documentation. We are currently testing methods to support SBML specification of ODE models in the cell agents (e.g., via libRoadrunner [48]), but until SBML is supported, we do not provide templates to integrate ODE models into PhysiCell functions to alter cell phenotype.
The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.
The choice of software capable of building chemical structures in three dimensions is far smaller. There are existing commercial packages, such as CAChe/Scigress [10], ChemBio3D [11], GaussView [12], HyperChem [13], CrystalMaker [14], Materials Studio [15], and Spartan [16], which are polished and capable of constructing many different types of molecular structures. They are, however, not available for all operating systems (most of them only run on Microsoft Windows), and are not easily extensible, customized, or integrated into automated workflows. Licensing costs can be prohibitive. If the company were to change its direction or focus, this can lead to a loss of a significant research investment in a commercial product. Furthermore, in most cases, these programs use custom, proprietary file formats, and semantic and chemical data can be lost in conversion to other data formats.
Broad goals for the design of a molecular editor were identified following a case study of the available applications. One of the main issues with both commercial and open-source applications is a lack of extensibility; many of the applications also only work on one or two operating systems. The creation of an open and extensible framework that implements many of the necessary foundations for a molecular builder and visualizer would facilitate more effective research in this area. Further, the open, standardized Chemical Markup Language (CML) file format [19, 20] would be used, to secure semantic and chemical data and allow easy interoperability with other chemistry software.
Currently, two upcoming versions of Avogadro are under development. The first is Avogadro version 1.1, which adds additional features and refinement, particularly including crystallography support developed through the XtalOpt project. The second is a more substantial development for Avogadro version 2.0, where many of the core data structures are being rewritten in order to offer greater flexibility and scalability. Our goal is to support an increasing scope of chemical systems, including biomolecules (DNA, RNA, saccarides, etc.), materials (crystallography, polymers, surfaces), nanoscience (nanoparticles, nanotubes, graphene, etc.) with improved speed, intuitive ease-of-use and simpler non-reciprocal licensing terms.
External PostgreSQL databases require you to provide database connection parameters. You must set the required connection keys in the openshift_management_template_parameters parameter in your inventory. The following keys are required:
This example overrides the persistent volume (PV) sizes. PV sizes must be set via openshift_management_template_parameters, which ensures that the application and database are able to make claims on created PVs without interfering with each other:
Indigenous knowledge (IK) refers to the understandings, skills and philosophies developed by societies with long histories of interaction with their natural surroundings. Local knowledge (LK) refers to the understandings and skills developed by individuals and populations, specific to the place where they live. These forms of knowledge, jointly referred to as Indigenous and Local Knowledge or ILK, are often highly context specific and embedded in local institutions, providing biological and ecosystem knowledge with landscape information. For example, they can contribute to effective land management, predictions of natural disasters, and identification of longer-term climate changes, and ILK can be particularly useful where formal data collection on environmental conditions may be sparse. ILK is often dynamic, with knowledge holders often experimenting with mixes of local and scientific approaches. Water management, soil fertility practices, grazing systems, restoration and sustainable harvesting of forests, and ecosystem-based adaptation are many of the land management practices often informed by ILK. ILK can also be used as an entry point for climate adaptation by balancing past experiences with new ways to cope. To be effective, initiatives need to take into account the differences in power between the holders of different types of knowledge. For example, including indigenous and/ or local people in programmes related to environmental conservation, formal education, land management planning and security tenure rights is key to facilitate climate change adaptation. Formal education is necessary to enhance adaptive capacity of ILK, since some researchers have suggested that these knowledge systems may become less relevant in certain areas where the rate of environmental change is rapid and the transmission of ILK between generations is becoming weaker.
Measuring progress towards goals is important in decision-making and adaptive governance to create common understanding and advance policy effectiveness (high agreement, medium evidence). Measurable indicators, selected with the participation of people and supporting data collection, are useful for climate policy development and decision-making. Indicators include the SDGs, nationally determined contributions (NDCs), land degradation neutrality (LDN) core indicators, carbon stock measurement, measurement and monitoring for REDD+, metrics for measuring biodiversity and ecosystem services, and governance capacity. 7.5.5, 7.5.7, 7.6.4, 7.6.6
The complex spatial, cultural and temporal dynamics of risk and uncertainty in relation to land and climate interactions and food security, require a flexible, adaptive, iterative approach to assessing risks, revising decisions and policy instruments (high confidence). Adaptive, iterative decision making moves beyond standard economic appraisal techniques to new methods such as dynamic adaptation pathways with risks identified by trigger points through indicators. Scenarios can provide valuable information at all planning stages in relation to land, climate and food; adaptive management addresses uncertainty in scenario planning with pathway choices made and reassessed to respond to new information and data as it becomes available. 3.7.5, 7.4.4, 7.5.2, 7.5.3, 7.5.4, 7.5.7, 7.6.1, 7.6.3
Indigenous and local knowledge (ILK) can play a key role in understanding climate processes and impacts, adaptation to climate change, sustainable land management (SLM) across different ecosystems, and enhancement of food security (high confidence). ILK is context-specific, collective, informally transmitted, and multi-functional, and can encompass factual information about the environment and guidance on management of resources and related rights and social behaviour. ILK can be used in decision-making at various scales and levels, and exchange of experiences with adaptation and mitigation that include ILK is both a requirement and an entry strategy for participatory climate communication and action. Opportunities exist for integration of ILK with scientific knowledge. 7.4.1, 7.4.5, 7.4.6, 7.6.4, Cross-Chapter Box 13 in Chapter 7 2ff7e9595c
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