scholarly journals TranSyT, the Transport Systems Tracker

2021 ◽  
Author(s):  
Davide Lagoa ◽  
José Lopes Faria ◽  
Filipe Liu ◽  
Emanuel Cunha ◽  
Christopher Henry ◽  
...  
Keyword(s):  
Software Development ◽  
Transport Proteins ◽  
Data Sources ◽  
Transport Systems ◽  
Rate Of Development ◽  
Manual Curation ◽  
Automatic Integration ◽  
Complete Genomes ◽  
Internal Database

The importance and rate of development of GSM models have been growing for the last years, increasing the demand for software solutions that automatise several steps of this process. However, since TRIAGE's release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. Unlike its predecessor, TranSyT does not rely on manual curation to expand its internal database, derived from highly-curated records retrieved from TCDB and complemented with information from other data sources. TranSyT compiles information regarding TC families, transport proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.

scholarly journals GrimoireLab: A toolset for software development analytics

2021 ◽  
Vol 7 ◽  
pp. e601
Author(s):  
Santiago Dueñas ◽  
Valerio Cosentino ◽  
Jesus M. Gonzalez-Barahona ◽  
Alvaro del Castillo San Felix ◽  
Daniel Izquierdo-Cortazar ◽  
...  
Keyword(s):  
Software Development ◽  
Preliminary Analysis ◽  
Data Retrieval ◽  
Mining Software Repositories ◽  
Data Sources ◽  
Data Sets ◽  
Community Based ◽  
Academic Environments ◽  
Software Repositories ◽  
Main Components

Background After many years of research on software repositories, the knowledge for building mature, reusable tools that perform data retrieval, storage and basic analytics is readily available. However, there is still room to improvement in the area of reusable tools implementing this knowledge. Goal To produce a reusable toolset supporting the most common tasks when retrieving, curating and visualizing data from software repositories, allowing for the easy reproduction of data sets ready for more complex analytics, and sparing the researcher or the analyst of most of the tasks that can be automated. Method Use our experience in building tools in this domain to identify a collection of scenarios where a reusable toolset would be convenient, and the main components of such a toolset. Then build those components, and refine them incrementally using the feedback from their use in both commercial, community-based, and academic environments. Results GrimoireLab, an efficient toolset composed of five main components, supporting about 30 different kinds of data sources related to software development. It has been tested in many environments, for performing different kinds of studies, and providing different kinds of services. It features a common API for accessing the retrieved data, facilities for relating items from different data sources, semi-structured storage for easing later analysis and reproduction, and basic facilities for visualization, preliminary analysis and drill-down in the data. It is also modular, making it easy to support new kinds of data sources and analysis. Conclusions We present a mature toolset, widely tested in the field, that can help to improve the situation in the area of reusable tools for mining software repositories. We show some scenarios where it has already been used. We expect it will help to reduce the effort for doing studies or providing services in this area, leading to advances in reproducibility and comparison of results.

scholarly journals BIG DATA FOR RISK ANALYSIS: THE FUTURE OF SAFE RAILWAYS

2016 ◽  
Author(s):  
Miguel Figueres Esteban
Keyword(s):  
Big Data ◽  
Risk Analysis ◽  
Safety Management ◽  
New Technology ◽  
Data Sources ◽  
Transport Systems ◽  
Text Documents ◽  
Railway Systems ◽  
Wide Range ◽  
Three Components

New technology brings ever more data to support decision-making for intelligent transport systems. Big Data is no longer a futuristic challenge, it is happening right now: modern railway systems have countless sources of data providing a massive quantity of diverse information on every aspect of operations such as train position and speed, brake applications, passenger numbers, status of the signaling system or reported incidents.The traditional approaches to safety management on the railways have relied on static data sources to populate traditional safety tools such as bow-tie models and fault trees. The Big Data Risk Analysis (BDRA) program for Railways at the University of Huddersfield is investigating how the many Big Data sources from the railway can be combined in a meaningful way to provide a better understanding about the GB railway systems and the environment within which they operate.Moving to BDRA is not simply a matter of scaling-up existing analysis techniques. BDRA has to coordinate and combine a wide range of sources with different types of data and accuracy, and that is not straight-forward. BDRA is structured around three components: data, ontology and visualisation. Each of these components is critical to support the overall framework. This paper describes how these three components are used to get safety knowledge from two data sources by means of ontologies from text documents. This is a part of the ongoing BDRA research that is looking at integrating many large and varied data sources to support railway safety and decision-makers.DOI: http://dx.doi.org/10.4995/CIT2016.2016.1825

Bile Salt Transporters: Molecular Characterization, Function, and Regulation

2003 ◽  
Vol 83 (2) ◽  
pp. 633-671 ◽  
Author(s):  
Michael Trauner ◽  
James L. Boyer
Keyword(s):  
Bile Salt ◽  
Molecular Characterization ◽  
Bile Salts ◽  
Organic Anion ◽  
Transport Proteins ◽  
Salt Transport ◽  
Transport Systems ◽  
Cholestatic Liver Disease ◽  
Bile Salt Transporters ◽  
Bile Salt Transport

Molecular medicine has led to rapid advances in the characterization of hepatobiliary transport systems that determine the uptake and excretion of bile salts and other biliary constituents in the liver and extrahepatic tissues. The bile salt pool undergoes an enterohepatic circulation that is regulated by distinct bile salt transport proteins, including the canalicular bile salt export pump BSEP (ABCB11), the ileal Na+-dependent bile salt transporter ISBT (SLC10A2), and the hepatic sinusoidal Na+- taurocholate cotransporting polypeptide NTCP (SLC10A1). Other bile salt transporters include the organic anion transporting polypeptides OATPs (SLC21A) and the multidrug resistance-associated proteins 2 and 3 MRP2,3 (ABCC2,3). Bile salt transporters are also present in cholangiocytes, the renal proximal tubule, and the placenta. Expression of these transport proteins is regulated by both transcriptional and posttranscriptional events, with the former involving nuclear hormone receptors where bile salts function as specific ligands. During bile secretory failure (cholestasis), bile salt transport proteins undergo adaptive responses that serve to protect the liver from bile salt retention and which facilitate extrahepatic routes of bile salt excretion. This review is a comprehensive summary of current knowledge of the molecular characterization, function, and regulation of bile salt transporters in normal physiology and in cholestatic liver disease and liver regeneration.

COMPUTATIONAL CONSTRUCTION OF SPECIALIZED BIOLOGICAL NETWORKS

2013 ◽  
Vol 11 (01) ◽  
pp. 1340003 ◽  
Author(s):  
HANG-MAO LEE ◽  
KARL-JOSEF DIETZ ◽  
RALF HOFESTÄDT
Keyword(s):  
Biological Networks ◽  
Retrieval System ◽  
Biological Network ◽  
Relevant Literature ◽  
Database Systems ◽  
Document Retrieval ◽  
Network Reduction ◽  
Manual Curation ◽  
Automatic Integration ◽  
Computer Scientists

Today we have access to more than 1500 molecular database systems inside the internet. Based on these databases and information systems, computer scientists developed and implemented different methods for the automatic integration and prediction of biological networks. The idea is to use such methods for the automatic prediction and expansion of rudimentary molecular knowledge. However, the inherent data deficiency problem concerning the properties of specialized network hampers the database- and text-mining-based network construction. This paper presents the concept concerning the computational network expansion, namely for the specific biological network–thiol-disulfide redox regulatory network. Besides, a network-contexted document retrieval system (ncDocReSy) is also introduced to assist the network reduction by providing indirectly relevant literature for user's manual curation. NcDocReSy combines literature search with biological network and ranks the retrieved literature according to the network topology. NcDocReSy is implemented as a Cytoscape plugin.

Computational Statistics of Data Science for Secured Software Engineering

2021 ◽  
pp. 81-96
Author(s):  
Raghavendra Rao Althar ◽  
Debabrata Samanta
Keyword(s):  
Software Engineering ◽  
Software Development ◽  
Language Processing ◽  
Data Science ◽  
Systems Development ◽  
Data Sources ◽  
Software Systems ◽  
Computational Statistics ◽  
Critical Dimensions ◽  
Work Done

The chapter focuses on exploring the work done for applying data science for software engineering, focusing on secured software systems development. With requirements management being the first stage of the life cycle, all the approaches that can help security mindset right at the beginning are explored. By exploring the work done in this area, various key themes of security and its data sources are explored, which will mark the setup of base for advanced exploration of the better approaches to make software systems mature. Based on the assessments of some of the work done in this area, possible prospects are explored. This exploration also helps to emphasize the key challenges that are causing trouble for the software development community. The work also explores the possible collaboration across machine learning, deep learning, and natural language processing approaches. The work helps to throw light on critical dimensions of software development where security plays a key role.

Towards using self-generated data sources to decision support in agile software development

2021 ◽  
Author(s):  
Maria de los Angeles German Vazquez ◽  
Gilberto Borrego Soto ◽  
Ramon Rene Palacios Cinco
Keyword(s):  
Decision Support ◽  
Software Development ◽  
Agile Software Development ◽  
Data Sources ◽  
Agile Software

Big Data: A Strategic Perspective

2014 ◽  
Vol 08 (03) ◽  
pp. 319-333
Author(s):  
David Alfred Ostrowski
Keyword(s):  
Big Data ◽  
Software Development ◽  
Data Sources ◽  
Apache Hadoop ◽  
Big Data Applications ◽  
Programming Techniques ◽  
Future Direction ◽  
Strategic Perspective ◽  
New Applications

Big Data has become ubiquitous across all areas of research allowing for new applications that were not possible earlier. Unlike software development relying on traditional data sources, Big Data applications present their own unique challenges to appropriately harness the utility of the Apache Hadoop architecture. In this paper, we introduce fundamental concepts of Hadoop and explore its usage as well as future direction. We also present our strategy for exploring the Hadoop architecture including addressing issues of scalability, customization of code and utilization of programming techniques.

scholarly journals Evolution of Plant Na+-P-Type ATPases: From Saline Environments to Land Colonization

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 221
Author(s):  
Siarhei A. Dabravolski ◽  
Stanislav V. Isayenkov
Keyword(s):  
Binding Site ◽  
Common Ancestor ◽  
Domain Architecture ◽  
Transport Proteins ◽  
Transport Systems ◽  
Α Subunit ◽  
Land Colonization ◽  
Major Factors ◽  
Membrane Pumps ◽  
P Type

Soil salinity is one of the major factors obstructing the growth and development of agricultural crops. Eukaryotes have two main transport systems involved in active Na+ removal: cation/H+ antiporters and Na+-P-type ATPases. Key transport proteins, Na+/K+-P-ATPases, are widely distributed among the different taxa families of pumps which are responsible for keeping cytosolic Na+ concentrations below toxic levels. Na+/K+-P-ATPases are considered to be absent in flowering plants. The data presented here are a complete inventory of P-type Na+/K+-P-ATPases in the major branches of the plant kingdom. We also attempt to elucidate the evolution of these important membrane pumps in plants in comparison with other organisms. We were able to observe the gradual replacement of the Na+-binding site to the Ca2+-binding site, starting with cyanobacteria and moving to modern land plants. Our results show that the α-subunit likely evolved from one common ancestor to bacteria, fungi, plants, and mammals, whereas the β-subunit did not evolve in green algae. In conclusion, our results strongly suggest the significant differences in the domain architecture and subunit composition of plant Na+/K+-P-ATPases depending on plant taxa and the salinity of the environment. The obtained data clarified and broadened the current views on the evolution of Na+/K+-P-ATPases. The results of this work would be helpful for further research on P-type ATPase functionality and physiological roles.

scholarly journals Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species

2021 ◽  
pp. 1-15
Author(s):  
Hassan Zafar ◽  
Milton H. Saier Jr.
Keyword(s):  
Human Health ◽  
Drug Targets ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Transport Proteins ◽  
Host Cells ◽  
Transport Systems ◽  
Ecological Niches ◽  
Beneficial Effects ◽  
Secondary Carriers

The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. <i>Bifidobacterium</i> species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: <i>B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum</i> subsp. <i>infantis, B. longum</i> subsp. <i>longum, and B. pseudocatenulatum</i>. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, <i>B. bifidum</i>, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of <i>Bacteroides, Escherichia coli/Salmonella</i>, and <i>Lactobacillus</i>. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.

scholarly journals Plant transporters involved in combating boron toxicity: beyond 3D structures

2020 ◽  
Vol 48 (4) ◽  
pp. 1683-1696
Author(s):  
Maria Hrmova ◽  
Matthew Gilliham ◽  
Stephen D. Tyerman
Keyword(s):  
Cell Biology ◽  
100Th Anniversary ◽  
Transport Proteins ◽  
Transport Systems ◽  
Boron Toxicity ◽  
Soil Conditions ◽  
Toxic Substances ◽  
Current State ◽  
Whole Plant ◽  
Adverse Environmental Conditions

Membrane transporters control the movement and distribution of solutes, including the disposal or compartmentation of toxic substances that accumulate in plants under adverse environmental conditions. In this minireview, in the light of the approaching 100th anniversary of unveiling the significance of boron to plants (K. Warington, 1923; Ann. Bot.37, 629) we discuss the current state of the knowledge on boron transport systems that plants utilise to combat boron toxicity. These transport proteins include: (i) nodulin-26-like intrinsic protein-types of aquaporins, and (ii) anionic efflux (borate) solute carriers. We describe the recent progress made on the structure–function relationships of these transport proteins and point out that this progress is integral to quantitative considerations of the transporter's roles in tissue boron homeostasis. Newly acquired knowledge at the molecular level has informed on the transport mechanics and conformational states of boron transport systems that can explain their impact on cell biology and whole plant physiology. We expect that this information will form the basis for engineering transporters with optimised features to alleviate boron toxicity tolerance in plants exposed to suboptimal soil conditions for sustained food production.

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