scholarly journals DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

2019 ◽  
Author(s):  
Onur Yukselen ◽  
Osman Turkyilmaz ◽  
Ahmet Rasit Ozturk ◽  
Manuel Garber ◽  
Alper Kucukural
Keyword(s):  
User Interface ◽  
Data Processing ◽  
Programming Languages ◽  
High Throughput ◽  
High Performance ◽  
Scientific Discovery ◽  
Biological Research ◽  
Wide Range ◽  
The Face ◽  
Economic Constraints

ABSTRACTThe emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research. The dramatic increase in the volume of data makes analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for a highly-parallel, flexible, portable, and reproducible data processing frameworks. Flexibility ensures that pipelines can support a variety of applications without requiring one-off modifications. Portability ensures that users can leverage computationally available resources and work within economic constraints. Reproducibility warrants credibility to the results and is particularly challenging in the face of the sheer volume of data and the complexity of processing pipelines that vary widely between users.Several platforms currently exist for the design and execution of complex pipelines (e.g. Galaxy, GenePattern, GeneProf). Unfortunately, these platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, Nextflow was implemented to simplify portable, scalable, and reproducible scientific pipelines using containers. We have used Nextflow capabilities as leverage and developed a user interface, DolphinNext, for creating, deploying, and executing complex Nextflow pipelines for high throughput data processing. The guiding principle of DolphinNext is to facilitate the building and deployment of complex pipelines using a modular approach implemented in a graphical interface. DolphinNext provides: 1. A drag and drop user interface that abstracts pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. A user interface to monitor pipeline execution that allows the re-initiation of pipelines at intermediate steps 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Seamless portability to distributed computational environments such as high-performance clusters or cloud computing environments.

scholarly journals Polyglot Programming in Applications Used for Genetic Data Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Robert M. Nowak
Keyword(s):  
Data Analysis ◽  
User Interface ◽  
Data Processing ◽  
Programming Languages ◽  
High Performance ◽  
Genetic Data ◽  
Web Browser ◽  
Data Process ◽  
Genetic Data Analysis

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

scholarly journals SraTailor: GUI software for visualizing high-throughput sequence read archives

2014 ◽  
Author(s):  
Shinya Oki ◽  
Kazumitsu Maehara ◽  
Yasuyuki Ohkawa ◽  
Chikara Meno
Keyword(s):  
User Interface ◽  
Data Processing ◽  
High Throughput ◽  
Graphical User Interface ◽  
Software Package ◽  
Sequence Data ◽  
Command Line ◽  
Accession Number ◽  
Wide Range

Raw high-throughput sequence data are deposited in public databases as SRAs (Sequence Read Archives) and are publically available to every researcher. However, in order to graphically visualize the sequence data of interest, the corresponding SRAs must be downloaded and converted into BigWig format through complicated command-line processing. This task requires users to possess skill with script languages and sequence data processing, a requirement that prevents a wide range of biologists from exploiting SRAs. To address these challenges, we developed SraTailor, a GUI (Graphical User Interface) software package that automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of SraTailor: entering an accession number of an SRA and clicking the mouse are the only steps required in order to obtain BigWig-formatted files and to graphically visualize the extents of reads at given loci. SraTailor is also able to make peak calls and files of other formats, and the software also accepts various command-line-like options. Therefore, this software makes SRAs fully exploitable by a wide range of biologists. SraTailor is freely available at http://www.dev.med.kyushu-u.ac.jp/sra_tailor/.

scholarly journals Current High-Throughput Approaches of Screening Modulatory Effects of Xenobiotics on Cytochrome P450 (CYP) Enzymes

2018 ◽  
Vol 7 (4) ◽  
pp. 29 ◽  
Author(s):  
Yee Ung ◽  
Chin Ong ◽  
Yan Pan
Keyword(s):  
Cytochrome P450 ◽  
High Throughput ◽  
Enzyme Activities ◽  
High Throughput Screening ◽  
High Performance ◽  
Screening Methods ◽  
Drug Metabolizing Enzyme ◽  
Enzyme Superfamily ◽  
Wide Range ◽  
Metabolizing Enzyme

Cytochrome P450 (CYP) is a critical drug-metabolizing enzyme superfamily. Modulation of CYP enzyme activities has the potential to cause drug–drug/herb interactions. Drug–drug/herb interactions can lead to serious adverse drug reactions (ADRs) or drug failures. Therefore, there is a need to examine the modulatory effects of new drug entities or herbal preparations on a wide range of CYP isoforms. The classic method of quantifying CYP enzyme activities is based on high-performance liquid chromatography (HPLC), which is time- and reagent-consuming. In the past two decades, high-throughput screening methods including fluorescence-based, luminescence-based, and mass-spectrometry-based assays have been developed and widely applied to estimate CYP enzyme activities. In general, these methods are faster and use lower volume of reagents than HPLC. However, each high-throughput method has its own limitations. Investigators may make a selection of these methods based on the available equipment in the laboratory, budget, and enzyme sources supplied. Furthermore, the current high-throughput systems should look into developing a reliable automation mechanism to accomplish ultra-high-throughput screening in the near future.

scholarly journals Geospatial Information Processing Technologies

2019 ◽  
pp. 191-227
Author(s):  
Zhenlong Li ◽  
Zhipeng Gui ◽  
Barbara Hofer ◽  
Yan Li ◽  
Simon Scheider ◽  
...  
Keyword(s):  
Information Processing ◽  
High Performance ◽  
Scientific Discovery ◽  
Geospatial Data ◽  
Geospatial Information ◽  
Processing Technologies ◽  
Digital Earth ◽  
Wide Range ◽  
Efficient Processing ◽  
Key Techniques

Abstract The increasing availability of geospatial data offers great opportunities for advancing scientific discovery and practices in society. Effective and efficient processing of geospatial data is essential for a wide range of Digital Earth applications such as climate change, natural hazard prediction and mitigation, and public health. However, the massive volume, heterogeneous, and distributed nature of global geospatial data pose challenges in geospatial information processing and computing. This chapter introduces three technologies for geospatial data processing: high-performance computing, online geoprocessing, and distributed geoprocessing, with each technology addressing one aspect of the challenges. The fundamental concepts, principles, and key techniques of the three technologies are elaborated in detail, followed by examples of applications and research directions in the context of Digital Earth. Lastly, a Digital Earth reference framework called discrete global grid system (DGGS) is discussed.

scholarly journals Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes

2016 ◽  
Author(s):  
C.J. Forman ◽  
H. Tomes ◽  
B. Mbobo ◽  
T. Baden ◽  
J.V. Raimondo
Keyword(s):  
Hippocampal Neurons ◽  
High Performance ◽  
Low Cost ◽  
Biological Research ◽  
Physical Sciences ◽  
Chemical Systems ◽  
Commercial System ◽  
Open Hardware ◽  
Wide Range ◽  
Two Photon Fluorescence

AbstractThe ability to reliably and precisely deliver picolitre volumes is an important component of biological research. Here we describe a high-performance, low-cost, open hardware pressure ejection system (Openspritzer), which can be constructed from off the shelf components. When connected to a standard micro-pipette via suitable pneumatic tubing, the device is capable of delivering minute doses of reagents to a wide range of biological and chemical systems. In this work, we characterise the performance of the device and compare it to a popular commercial system using two-photon fluorescence microscopy. We found that Openspritzer provides the same level of control over delivered reagent dose as the commercial system. Next, we demonstrate the utility of Openspritzer in a series of standard neurobiological applications. First, we used Openspritzer to deliver precise amounts of the neurotransmitters glutamate and GABA to hippocampal neurons to elicit time- and dose-precise excitatory and inhibitory responses, respectively. Second, we used Openspritzer to deliver infectious viral and bacterial agents to living tissue. Viral transfection of hippocampal interneurons with channelrhodopsin allowed for the optogenetic manipulation of hippocampal circuitry with light. Finally, we successfully used Openspritzer to infect organotypic hippocampal slice cultures with fluorescent Mycobacterium bovis bacilli. We anticipate that due to its high performance and low cost Openspritzer will be of interest to a broad range of researchers working in the life and physical sciences.

scholarly journals Micro-Magellan: A flexible, open source acquisition software for high throughput biological light microscopy

2016 ◽  
Author(s):  
Henry Pinkard ◽  
Nico Stuurman ◽  
Kaitlin Corbin ◽  
Ronald Vale ◽  
Matthew F Krummel
Keyword(s):  
User Interface ◽  
Light Microscopy ◽  
Open Source ◽  
High Throughput ◽  
Biological Samples ◽  
Abstraction Layer ◽  
Wide Range ◽  
Automated Imaging ◽  
Hardware Abstraction Layer ◽  
High Throughput Imaging

We demonstrate the capabilities of μMagellan: a flexible, open source microscopy software for reproducible high throughput imaging of biological samples across heterogeneous scales of space and time. μMagellan provides a simple user interface for exploration and automated imaging of non-cuboidal regions. By utilizing the hardware abstraction layer of μManager, μMagellan provides a powerful and extensible platform for imaging heterogeneous biological samples on a wide range of existing microscopes.

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

Validated Stability Indicating HPTLC Method for the Estimation of Amoxapine in Different Stress Conditions

2019 ◽  
Vol 15 (3) ◽  
pp. 273-279
Author(s):  
Shweta G. Rangari ◽  
Nishikant A. Raut ◽  
Pradip W. Dhore
Keyword(s):  
High Performance ◽  
Limit Of Detection ◽  
Degradation Products ◽  
Analysis Data ◽  
Peak Height ◽  
Good Resolution ◽  
Stability Indicating ◽  
Limit Of Quantitation ◽  
Wide Range ◽  
Hptlc Method

Background:The unstable and/or toxic degradation products may form due to degradation of drug which results into loss of therapeutic activity and lead to life threatening condition. Hence, it is important to establish the stability characteristics of drug in various conditions such as in temperature, light, oxidising agent and susceptibility across a wide range of pH values.Introduction:The aim of the proposed study was to develop simple, sensitive and economic stability indicating high performance thin layer chromatography (HPTLC) method for the quantification of Amoxapine in the presence of degradation products.Methods:Amoxapine and its degraded products were separated on precoated silica gel 60F254 TLC plates by using mobile phase comprising of methanol: toluene: ammonium acetate (6:3:1, v/v/v). The densitometric evaluation was carried out at 320 nm in reflectance/absorbance mode. The degradation products obtained as per ICH guidelines under acidic, basic and oxidative conditions have different Rf values 0.12, 0.26 and 0.6 indicating good resolution from each other and pure drug with Rf: 0.47. Amoxapine was found to be stable under neutral, thermal and photo conditions.Results:The method was validated as per ICH Q2 (R1) guidelines in terms of accuracy, precision, ruggedness, robustness and linearity. A good linear relationship between concentration and response (peak area and peak height) over the range of 80 ng/spot to 720 ng/spot was observed from regression analysis data showing correlation coefficient 0.991 and 0.994 for area and height, respectively. The limit of detection (LOD) and limit of quantitation (LOQ) for area were found to be 1.176 ng/mL and 3.565 ng/mL, whereas for height, 50.063 ng/mL and 151.707 ng/mL respectively.Conclusion:The statistical analysis confirmed the accuracy, precision and selectivity of the proposed method which can be effectively used for the analysis of amoxapine in the presence of degradation products.

Phytochemical, Analytical and Medicinal Studies of Holoptelea integrifolia Roxb. Planch - A Review

2019 ◽  
Vol 5 (4) ◽  
pp. 270-277 ◽  
Author(s):  
Vijay Kumar ◽  
Simranjeet Singh ◽  
Ragini Bhadouria ◽  
Ravindra Singh ◽  
Om Prakash
Keyword(s):  
Liquid Chromatography ◽  
Thin Layer ◽  
Thin Layer Chromatography ◽  
High Performance ◽  
Biologically Active ◽  
Toxicological Studies ◽  
Wide Range ◽  
Layer Chromatography

Holoptelea integrifolia Roxb. Planch (HI) has been used to treat various ailments including obesity, osteoarthritis, arthritis, inflammation, anemia, diabetes etc. To review the major phytochemicals and medicinal properties of HI, exhaustive bibliographic research was designed by means of various scientific search engines and databases. Only 12 phytochemicals have been reported including biologically active compounds like betulin, betulinic acid, epifriedlin, octacosanol, Friedlin, Holoptelin-A and Holoptelin-B. Analytical methods including the Thin Layer Chromatography (TLC), High-Performance Thin Layer Chromatography (HPTLC), High-Performance Liquid Chromatography (HPLC) and Liquid Chromatography With Mass Spectral (LC-MS) analysis have been used to analyze the HI. From medicinal potency point of view, these phytochemicals have a wide range of pharmacological activities such as antioxidant, antibacterial, anti-inflammatory, and anti-tumor. In the current review, it has been noticed that the mechanism of action of HI with biomolecules has not been fully explored. Pharmacology and toxicological studies are very few. This seems a huge literature gap to be fulfilled through the detailed in-vivo and in-vitro studies.

scholarly journals RELaTED Project: New Developments on Ultra-Low Temperature District Heating Networks

Proceedings ◽  
2020 ◽  
Vol 65 (1) ◽  
pp. 25
Author(s):  
Antonio Garrido Marijuan ◽  
Roberto Garay ◽  
Mikel Lumbreras ◽  
Víctor Sánchez ◽  
Olga Macias ◽  
...  
Keyword(s):  
Low Temperature ◽  
High Performance ◽  
Waste Heat ◽  
District Heating ◽  
Hot Water ◽  
Thermal Systems ◽  
Heating Source ◽  
Wide Range ◽  
Thermal Sources ◽  
Heating Networks

District heating networks deliver around 13% of the heating energy in the EU, being considered as a key element of the progressive decarbonization of Europe. The H2020 REnewable Low TEmperature District project (RELaTED) seeks to contribute to the energy decarbonization of these infrastructures through the development and demonstration of the following concepts: reduction in network temperature down to 50 °C, integration of renewable energies and waste heat sources with a novel substation concept, and improvement on building-integrated solar thermal systems. The coupling of renewable thermal sources with ultra-low temperature district heating (DH) allows for a bidirectional energy flow, using the DH as both thermal storage in periods of production surplus and a back-up heating source during consumption peaks. The ultra-low temperature enables the integration of a wide range of energy sources such as waste heat from industry. Furthermore, RELaTED also develops concepts concerning district heating-connected reversible heat pump systems that allow to reach adequate thermal levels for domestic hot water as well as the use of the network for district cooling with high performance. These developments will be demonstrated in four locations: Estonia, Serbia, Denmark, and Spain.

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