2,470 research outputs found

    Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

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    BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download

    Standard Operating Procedure and Workplan for the Terrestrial Environmental Observation Network (TEON) – Arctic Landscape Conservation Cooperative: Kuparuk River Basin and Adjacent Catchments

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    TABLE OF CONTENTS ................................................................................................................. i DISCLAIMER ................................................................................................................................ ii CONVERSION FACTORS, UNITS, WATER QUALITY UNITS, VERTICAL AND HORIZONTAL DATUM, ABBREVIATIONS AND SYMBOLS .............................................. iii 1 INTRODUCTION .................................................................................................................. 1 2 STATION HISTORY ............................................................................................................. 5 3 DATA COLLECTION METHODS ....................................................................................... 8 3.1 Air Temperature and Relative Humidity ........................................................................ 12 3.2 Wind Speed and Direction ............................................................................................. 14 3.3 Radiation ........................................................................................................................ 15 3.3.1 Net Radiation .......................................................................................................... 15 3.3.2 Shortwave Radiation ............................................................................................... 16 3.3.3 Longwave Radiation ............................................................................................... 17 3.4 Summer Precipitation ..................................................................................................... 18 3.5 Snow Depth .................................................................................................................... 18 3.6 Field Snow Survey ......................................................................................................... 20 3.7 Water Levels .................................................................................................................. 21 3.8 Discharge Measurements ............................................................................................... 23 3.8.1 Acoustic Doppler Current Profiler .......................................................................... 25 4 STATION TELEMETRY ..................................................................................................... 28 5 DATALOGGER PROGRAM .............................................................................................. 30 6 METADATA ........................................................................................................................ 31 7 QUALITY CONTROL AND DATA PROCESSING .......................................................... 32 8 DATA REPORTING AND ARCHIVING ........................................................................... 33 9 REFERENCES ..................................................................................................................... 36 10 APPENDIX LIST ................................................................................................................. 3

    ELM: the status of the 2010 eukaryotic linear motif resource

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    Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a ‘Bar Code’ format, which also displays known instances from homologous proteins through a novel ‘Instance Mapper’ protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation

    Orbital operation study. Volume 3: Basic vehicle summaries

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    The vehicle related data developed during the orbital operations study are described. The interfacing activity findings have been realigned into the four basic vehicle systems as follows: (1) earth orbital shuttle (EOS), (2) research and applications module (RAM), (3) space based, ground based, manned and unmanned tugs, and (4) modular space station (MSS)

    Knowledge Management Approaches for predicting Biomarker and Assessing its Impact on Clinical Trials

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    The recent success of companion diagnostics along with the increasing regulatory pressure for better identification of the target population has created an unprecedented incentive for the drug discovery companies to invest into novel strategies for stratified biomarker discovery. Catching with this trend, trials with stratified biomarker in drug development have quadrupled in the last decade but represent a small part of all Interventional trials reflecting multiple co-developmental challenges of therapeutic compounds and companion diagnostics. To overcome the challenge, varied knowledge management and system biology approaches are adopted in the clinics to analyze/interpret an ever increasing collection of OMICS data. By semi-automatic screening of more than 150,000 trials, we filtered trials with stratified biomarker to analyse their therapeutic focus, major drivers and elucidated the impact of stratified biomarker programs on trial duration and completion. The analysis clearly shows that cancer is the major focus for trials with stratified biomarker. But targeted therapies in cancer require more accurate stratification of patient population. This can be augmented by a fresh approach of selecting a new class of biomolecules i.e. miRNA as candidate stratification biomarker. miRNA plays an important role in tumorgenesis in regulating expression of oncogenes and tumor suppressors; thus affecting cell proliferation, differentiation, apoptosis, invasion, angiogenesis. miRNAs are potential biomarkers in different cancer. However, the relationship between response of cancer patients towards targeted therapy and resulting modifications of the miRNA transcriptome in pathway regulation is poorly understood. With ever-increasing pathways and miRNA-mRNA interaction databases, freely available mRNA and miRNA expression data in multiple cancer therapy have created an unprecedented opportunity to decipher the role of miRNAs in early prediction of therapeutic efficacy in diseases. We present a novel SMARTmiR algorithm to predict the role of miRNA as therapeutic biomarker for an anti-EGFR monoclonal antibody i.e. cetuximab treatment in colorectal cancer. The application of an optimised and fully automated version of the algorithm has the potential to be used as clinical decision support tool. Moreover this research will also provide a comprehensive and valuable knowledge map demonstrating functional bimolecular interactions in colorectal cancer to scientific community. This research also detected seven miRNA i.e. hsa-miR-145, has-miR-27a, has- miR-155, hsa-miR-182, hsa-miR-15a, hsa-miR-96 and hsa-miR-106a as top stratified biomarker candidate for cetuximab therapy in CRC which were not reported previously. Finally a prospective plan on future scenario of biomarker research in cancer drug development has been drawn focusing to reduce the risk of most expensive phase III drug failures

    A General Concept for Consistent Documentation of Computational Analyses

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    The ever-growing amount of data in the field of life sciences demands standardized ways of high-throughput computational analysis. This standardization requires a thorough documentation of each step in the computational analysis to enable researchers to understand and reproduce the results. However, due to the heterogeneity in software setups and the high rate of change during tool development, reproducibility is hard to achieve. One reason is that there is no common agreement in the research community on how to document computational studies. In many cases, simple flat files or other unstructured text documents are provided by researchers as documentation, which are often missing software dependencies, versions and sufficient documentation to understand the workflow and parameter settings. As a solution we suggest a simple and modest approach for documenting and verifying computational analysis pipelines. We propose a two-part scheme that defines a computational analysis using a Process and an Analysis metadata document, which jointly describe all necessary details to reproduce the results. In this design we separate the metadata specifying the process from the metadata describing an actual analysis run, thereby reducing the effort of manual documentation to an absolute minimum. Our approach is independent of a specific software environment, results in human readable XML documents that can easily be shared with other researchers and allows an automated validation to ensure consistency of the metadata. Because our approach has been designed with little to no assumptions concerning the workflow of an analysis, we expect it to be applicable in a wide range of computational research fields. Database URL: http://deep.mpi-inf.mpg.de/DAC/cmds/pub/pyvalid.zi

    Sensitivity of Distress Rate to Observed Distress Levels

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    The New Mexico Department of Transportation (NMDOT) uses a composite pavement condition index to identify and rank roads for budgeting and scheduling repairs. NMDOT uses an index number called the Pavement Serviceability Index or PSI. A key component of this index number is the Distress Rate (DR) which is comprised of pavement distress severities and extents with a weighting factor assigned for each distress. Until 2013, NMDOT conducted pavement evaluations manually and in 2012 revised how pavement distress data were collected and evaluated. The two pavement distress collection procedures that were altered the most were for transverse cracking and alligator cracking. This research evaluates how sensitive the DR is to the revised data collection procedures. The comparison used a single milepost test section and one evaluator as ground truth data and then varied input values for a single item while holding all of the others constant to see what sort of influence the data had on the DR. The results confirmed that the DR has limited sensitivity due to the data ranges used for input to the composite DR index

    Human operator performance of remotely controlled tasks: Teleoperator research conducted at NASA's George C. Marshal Space Flight Center

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    The capabilities within the teleoperator laboratories to perform remote and teleoperated investigations for a wide variety of applications are described. Three major teleoperator issues are addressed: the human operator, the remote control and effecting subsystems, and the human/machine system performance results for specific teleoperated tasks
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