scholarly journals CurD: A Tool for Diffusion Analyses on Curved Membranes

2021 ◽  
Author(s):  
Balázs Fábián ◽  
Matti Javanainen
Keyword(s):  
Gaussian Curvature ◽  
Mean Curvature ◽  
Computational Studies ◽  
Command Line ◽  
Curved Surfaces ◽  
Living Matter ◽  
Command Line Interface ◽  
Lipid Packing ◽  
Propagation Algorithm ◽  
Curved Membranes

Curved membranes are abundant and functionally relevant in living matter, yet they have eluded computational studies due to methodological limitations. With multiple approaches available for setting up simulations on such curved membranes, there is a growing need for efficient and versatile tools to analyze their outcomes. Here, we present CurD, a freely available tool for analyzing the diffusion of membrane constituents along curved surfaces. The tool efficiently uses the Vertex-oriented Triangle Propagation algorithm to compute geodesic distances significantly faster than conventional implementations of path-finding algorithms, while providing a friendly command-line interface. With CurD, we resolve the effects of curvature and lipid packing densities on the diffusion of lipids on two curved membranes---one with only mean curvature and another with both Mean and Gaussian curvature. We find that Gaussian curvature plays a surprisingly small role, whereas mean curvature or packing of lipid headgroups largely dictates their mobility.

ESIS ON THE WORLD WIDE WEB

1994 ◽  
Vol 05 (05) ◽  
pp. 805-809 ◽  
Author(s):  
SALIM G. ANSARI ◽  
PAOLO GIOMMI ◽  
ALBERTO MICOL
Keyword(s):  
World Wide Web ◽  
Web Application ◽  
World Wide ◽  
Markup Language ◽  
Command Line ◽  
Command Line Interface ◽  
The World ◽  
Hypertext Transfer Protocol ◽  
Hypertext Markup Language ◽  
Near Future

On 3rd November, 1993, ESIS announced its Homepage on the World Wide Web (WWW) to the user community. Ever since then, ESIS has steadily increased its Web support to the astronomical community to include a bibliographic service, the ESIS catalogue documentation and the ESIS Data Browser. More functionality will be added in the near future. All these services share a common ESIS structure that is used by other ESIS user paradigms such as the ESIS Graphical User Interface (Giommi and Ansari, 1993), and the ESIS Command Line Interface. A forms-based paradigm, each ESIS-Web application interfaces to the hypertext transfer protocol (http) translating queries from/to the hypertext markup language (html) format understood by the NCSA Mosaic interface. In this paper, we discuss the ESIS system and show how each ESIS service works on the World Wide Web client.

scholarly journals UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

2021 ◽  
Vol 9 ◽  
Author(s):  
Caio Ribeiro ◽  
Lucas Oliveira ◽  
Romina Batista ◽  
Marcos De Sousa
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Phylogenetic Trees ◽  
Computational Analysis ◽  
Data Matrix ◽  
Command Line ◽  
Command Line Interface ◽  
Ultraconserved Elements ◽  
Research Software ◽  
Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

scholarly journals Efficient Transfer of data from RDBMS to HDFS and conversion to JSON format

2021 ◽  
Vol 9 (10) ◽  
pp. 1869-1871
Author(s):  
Dr. C. K. Gomathy
Keyword(s):  
Data Warehouse ◽  
Relational Databases ◽  
Command Line ◽  
Command Line Interface ◽  
Apache Hadoop ◽  
Enterprise Data Warehouse ◽  
Efficient Transfer ◽  
Efficient Execution

Abstract: Apache Sqoop is mainly used to efficiently transfer large volumes of data between Apache Hadoop and relational databases. It helps to certain tasks, such as ETL (Extract transform load) processing, from an enterprise data warehouse to Hadoop, for efficient execution at a much less cost. Here first we import the table which presents in MYSQL Database with the help of command-line interface application called Sqoop and there is a chance of addition of new rows and updating new rows then we have to execute the query again. So, with the help of our project there is no need of executing queries again for that we are using Sqoop job, which consists of total commands for import and next after import we retrieve the data from hive using Java JDBC and we convert the data to JSON Format, which consists of data in an organized way and easy to access manner by using GSON Library. Keywords: Sqoop, Json, Gson, Maven and JDBC

Model-Centric Fulfillment Operations and Maintenance Automation

2018 ◽  
pp. 1-20
Author(s):  
Patrick Moore
Keyword(s):  
Support Systems ◽  
Dynamic Capability ◽  
Command Line ◽  
Command Line Interface ◽  
Business Support ◽  
Service Models ◽  
Operations And Maintenance ◽  
Operational Models ◽  
Multiple Templates

As networks have evolved, there has been an evolution in how they are managed as well. This evolution has seen a move from manual configuration via command line interface (CLI) to script-based automation and eventually to a template-based approach with workflow to coordinate multiple templates and scripts. The next step in this evolution is the introduction of models to provide a more dynamic capability than is in place today. This chapter will discuss three major layers of modelling that should be considered during implementation of this approach: device models focused on the configuration of the hardware itself; service models focused on the customer or network facing services that leverage the hardware level configuration; and operational models focused on people, processes, and tools involved in application of device and service models. This includes the orchestration of activities with other tools, such as operational support systems (OSS) and business support systems (BSS).

scholarly journals BioKEEN: a library for learning and evaluating biological knowledge graph embeddings

2019 ◽  
Vol 35 (18) ◽  
pp. 3538-3540 ◽  
Author(s):  
Mehdi Ali ◽  
Charles Tapley Hoyt ◽  
Daniel Domingo-Fernández ◽  
Jens Lehmann ◽  
Hajira Jabeen
Keyword(s):  
Supplementary Information ◽  
Knowledge Graph ◽  
Biological Knowledge ◽  
Command Line ◽  
Graph Embeddings ◽  
Command Line Interface ◽  
Software Ecosystem ◽  
Mapping Resource ◽  
Significant Attention

Abstract Summary Knowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense representations for graphs’ nodes and edges. However, the software ecosystem for their application to bioinformatics remains limited and inaccessible for users without expertise in programing and machine learning. Therefore, we developed BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through an interactive command line interface. Finally, we present a case study in which we used a novel biological pathway mapping resource to predict links that represent pathway crosstalks and hierarchies. Availability and implementation BioKEEN and PyKEEN are open source Python packages publicly available under the MIT License at https://github.com/SmartDataAnalytics/BioKEEN and https://github.com/SmartDataAnalytics/PyKEEN Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Recent developments in theCCP-EMsoftware suite

2017 ◽  
Vol 73 (6) ◽  
pp. 469-477 ◽  
Author(s):  
Tom Burnley ◽  
Colin M. Palmer ◽  
Martyn Winn
Keyword(s):  
Easy Access ◽  
Software Framework ◽  
Command Line ◽  
Command Line Interface ◽  
Software Suite ◽  
Computational Support ◽  
Recent Developments ◽  
User Friendly ◽  
Different Levels ◽  
Friendly Graphical User Interface

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessibleviaa user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The currentCCP-EMsuite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.

scholarly journals Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Ralf C. Mueller ◽  
Nicolai Mallig ◽  
Jacqueline Smith ◽  
Lél Eöery ◽  
Richard I. Kuo ◽  
...  
Keyword(s):  
Bird Species ◽  
Gene Symbol ◽  
Immune Gene ◽  
Command Line ◽  
Biological Processes ◽  
Command Line Interface ◽  
Target List ◽  
Immune Genes ◽  
Front End ◽  
Gene Symbols

Abstract Background Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the “correct” set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K (“Bird 10,000 Genomes”) consortium’s whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm. Construction and content A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the “seed” for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database. Utility and discussion The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.

scholarly journals Umbilical points on surfaces in RN

1985 ◽  
Vol 100 ◽  
pp. 135-143 ◽  
Author(s):  
Kazuyuki Enomoto
Keyword(s):  
Gaussian Curvature ◽  
Mean Curvature ◽  
Curvature Vector ◽  
Mean Curvature Vector ◽  
Normal Connection ◽  
Round Sphere ◽  
Positive Gaussian Curvature ◽  
Connected Surface ◽  
Umbilical Points ◽  
The Mean

Let ϕ: M → RN be an isometric imbedding of a compact, connected surface M into a Euclidean space RN. ψ is said to be umbilical at a point p of M if all principal curvatures are equal for any normal direction. It is known that if the Euler characteristic of M is not zero and N = 3, then ψ is umbilical at some point on M. In this paper we study umbilical points of surfaces of higher codimension. In Theorem 1, we show that if M is homeomorphic to either a 2-sphere or a 2-dimensional projective space and if the normal connection of ψ is flat, then ψ is umbilical at some point on M. In Section 2, we consider a surface M whose Gaussian curvature is positive constant. If the surface is compact and N = 3, Liebmann’s theorem says that it must be a round sphere. However, if N ≥ 4, the surface is not rigid: For any isometric imbedding Φ of R3 into R4 Φ(S2(r)) is a compact surface of constant positive Gaussian curvature 1/r2. We use Theorem 1 to show that if the normal connection of ψ is flat and the length of the mean curvature vector of ψ is constant, then ψ(M) is a round sphere in some R3 ⊂ RN. When N = 4, our conditions on ψ is satisfied if the mean curvature vector is parallel with respect to the normal connection. Our theorem fails if the surface is not compact, while the corresponding theorem holds locally for a surface with parallel mean curvature vector (See Remark (i) in Section 3).

scholarly journals Modified Roller Coaster Surface in Space

Mathematics ◽  
2019 ◽  
Vol 7 (2) ◽  
pp. 195 ◽  
Author(s):  
Selçuk BAŞ ◽  
Talat KÖRPINAR
Keyword(s):  
Gaussian Curvature ◽  
Mean Curvature ◽  
Roller Coaster ◽  
Orthogonal Frame

In this paper, a new modified roller coaster surface according to a modified orthogonal frame is investigated in Euclidean 3-space. In this method, a new modified roller coaster surface is modeled. Both the Gaussian curvature and mean curvature of roller coaster surfaces are investigated. Subsequently, we obtain several characterizations in Euclidean 3-space.

scholarly journals Winding number selection on merons by Gaussian curvature’s sign

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo Gabriel Elías ◽  
Nicolás Vidal-Silva ◽  
Vagson L. Carvalho-Santos
Keyword(s):  
Gaussian Curvature ◽  
Domain Walls ◽  
Curved Surfaces ◽  
Two Dimensional ◽  
Winding Number ◽  
Direct Relation ◽  
Topological Properties ◽  
The Core ◽  
Magnetic Surfaces ◽  
The Relationship

Abstract We study the relationship between the winding number of magnetic merons and the Gaussian curvature of two-dimensional magnetic surfaces. We show that positive (negative) Gaussian curvatures privilege merons with positive (negative) winding number. As in the case of unidimensional domain walls, we found that chirality is connected to the polarity of the core. Both effects allow to predict the topological properties of metastable states knowing the geometry of the surface. These features are related with the recently predicted Dzyaloshinskii-Moriya emergent term of curved surfaces. The presented results are at our knowledge the first ones drawing attention about a direct relation between geometric properties of the surfaces and the topology of the hosted solitons.

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