scholarly journals OmixAnalyzer – A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets

2013 ◽  
pp. 46-53 ◽  
Author(s):  
Thomas Stoltmann ◽  
Karin Zimmermann ◽  
André Koschmieder ◽  
Ulf Leser
Keyword(s):  
High Throughput ◽  
Data Sets ◽  
Omics Data ◽  
Web Based ◽  
Web Based System

scholarly journals BioMiner: Paving the Way for Personalized Medicine

2015 ◽  
Vol 14 ◽  
pp. CIN.S20910 ◽  
Author(s):  
Chris Bauer ◽  
Karol Stec ◽  
Alexander Glintschert ◽  
Kristina Gruden ◽  
Christian Schichor ◽  
...  
Keyword(s):  
Personalized Medicine ◽  
High Throughput ◽  
Human Biology ◽  
Supplementary File ◽  
Data Sets ◽  
Omics Data ◽  
The Novel ◽  
Web Based ◽  
High Throughput Data ◽  
Interdisciplinary Project

Personalized medicine is promising a revolution for medicine and human biology in the 21st century. The scientific foundation for this revolution is accomplished by analyzing biological high-throughput data sets from genomics, transcriptomics, proteomics, and metabolomics. Currently, access to these data has been limited to either rather simple Web-based tools, which do not grant much insight or analysis by trained specialists, without firsthand involvement of the physician. Here, we present the novel Web-based tool “BioMiner,” which was developed within the scope of an international and interdisciplinary project (SYSTHER†) and gives access to a variety of high-throughput data sets. It provides the user with convenient tools to analyze complex cross-omics data sets and grants enhanced visualization abilities. BioMiner incorporates transcriptomic and cross-omics high-throughput data sets, with a focus on cancer. A public instance of BioMiner along with the database is available at http://systherDB.microdiscovery.de/ , login and password: “systher”; a tutorial detailing the usage of BioMiner can be found in the Supplementary File.

scholarly journals multiSLIDE: a web server for exploring connected elements of biological pathways in multi-omics data

2019 ◽  
Author(s):  
Soumita Ghosh ◽  
Abhik Datta ◽  
Hyungwon Choi
Keyword(s):  
Keyword Search ◽  
Data Sets ◽  
Omics Data ◽  
Web Based ◽  
Molecular Features ◽  
External Data ◽  
Cluster Data ◽  
Wide Range ◽  
Time Basis ◽  
Gene Ontologies

AbstractEmerging multi-omics experiments pose new challenges for exploration of quantitative data sets. We present multiSLIDE, a web-based interactive tool for simultaneous heatmap visualization of interconnected molecular features in multi-omics data sets. multiSLIDE operates by keyword search for visualizing biologically connected molecular features, such as genes in pathways and Gene Ontologies, offering convenient functionalities to rearrange, filter, and cluster data sets on a web browser in a real time basis. Various built-in querying mechanisms make it adaptable to diverse omics types, and visualizations are fully customizable. We demonstrate the versatility of the tool through three example studies, each of which showcases its applicability to a wide range of multi-omics data sets, ability to visualize the links between molecules at different granularities of measurement units, and the interface to incorporate inter-molecular relationship from external data sources into the visualization. Online and standalone versions of multiSLIDE are available at https://github.com/soumitag/multiSLIDE.

ChemInformatics Model Explorer (CIME): Exploratory analysis of chemical model explanations

2021 ◽  
Author(s):  
Christina Humer ◽  
Henry Heberle ◽  
Floriane Montanari ◽  
Thomas Wolf ◽  
Florian Huber ◽  
...  
Keyword(s):  
Machine Learning ◽  
Small Molecules ◽  
Small Molecule ◽  
Daily Basis ◽  
Data Sets ◽  
Visualization Tool ◽  
Web Based ◽  
Pharmacokinetic Properties ◽  
Opening Up ◽  
Web Based System

The introduction of machine learning to small molecule research – an inherently multidisciplinary field in which chemists and data scientists combine their expertise and collaborate – has been vital to making screening processes more efficient. In recent years, numerous models that predict pharmacokinetic properties or bioactivity have been published, and these are used on a daily basis by chemists to make decisions and prioritize ideas. The emerging field of explainable artificial intelligence is opening up new possibilities for understanding the reasoning that underlies a model. In small molecule research, this means relating contributions of substructures of compounds to their predicted properties, which in turn also allows the areas of the compounds that have the greatest influence on the outcome to be identified. However, there is no interactive visualization tool that facilitates such interdisciplinary collaborations towards interpretability of machine learning models for small molecules. To fill this gap, we present CIME (ChemInformatics Model Explorer), an interactive web-based system that allows users to inspect chemical data sets, visualize model explanations, compare interpretability techniques, and explore subgroups of compounds. The tool is model-agnostic and can be run on a server or a workstation.

scholarly journals multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Soumita Ghosh ◽  
Abhik Datta ◽  
Hyungwon Choi
Keyword(s):  
Keyword Search ◽  
Data Sets ◽  
Omics Data ◽  
Web Browser ◽  
Web Based ◽  
Molecular Features ◽  
Cluster Data ◽  
Wide Range ◽  
Or Genes ◽  
Simultaneous Visualization

AbstractQuantitative multi-omics data are difficult to interpret and visualize due to large volume of data, complexity among data features, and heterogeneity of information represented by different omics platforms. Here, we present multiSLIDE, a web-based interactive tool for the simultaneous visualization of interconnected molecular features in heatmaps of multi-omics data sets. multiSLIDE visualizes biologically connected molecular features by keyword search of pathways or genes, offering convenient functionalities to query, rearrange, filter, and cluster data on a web browser in real time. Various querying mechanisms make it adaptable to diverse omics types, and visualizations are customizable. We demonstrate the versatility of multiSLIDE through three examples, showcasing its applicability to a wide range of multi-omics data sets, by allowing users to visualize established links between molecules from different omics data, as well as incorporate custom inter-molecular relationship information into the visualization. Online and stand-alone versions of multiSLIDE are available at https://github.com/soumitag/multiSLIDE.

Rancang Bangun Sistem Penerimaan Dan Mutasi Barang Pada PDAM Tirta Kerta Raharja

Sensi Journal ◽  
2020 ◽  
Vol 6 (2) ◽  
pp. 236-246
Author(s):  
Ilamsyah Ilamsyah ◽  
Yulianto Yulianto ◽  
Tri Vita Febriani
Keyword(s):  
System Analysis ◽  
Object Oriented ◽  
Analysis Method ◽  
Web Based ◽  
Visual Modeling ◽  
Long Time ◽  
The Right ◽  
And Control ◽  
Web Based System ◽  
The Web

The right and appropriate system of receiving and transferring goods is needed by the company. In the process of receiving and transferring goods from the central warehouse to the branch warehouse at PDAM Tirta Kerta Raharja, Tangerang Regency, which is currently done manually is still ineffective and inaccurate because the Head of Subdivision uses receipt documents, namely PPBP and mutation of goods, namely MPPW in the form of paper as a submission media. The Head of Subdivision enters the data of receipt and mutation of goods manually and requires a relatively long time because at the time of demand for the transfer of goods the Head of Subdivision must check the inventory of goods in the central warehouse first. Therefore, it is necessary to hold a design of information systems for the receipt and transfer of goods from the central warehouse to a web-based branch warehouse that is already database so that it is more effective, efficient and accurate. With the web-based system of receiving and transferring goods that are already datatabed, it can facilitate the Head of Subdivision in inputing data on the receipt and transfer of goods and control of stock inventory so that the Sub Head of Subdivision can do it periodically to make it more effective, efficient and accurate. The method of data collection is done by observing, interviewing and studying literature from various previous studies, while the system analysis method uses the Waterfall method which aims to solve a problem and uses design methods with visual modeling that is object oriented with UML while programming using PHP and MySQL as a database.

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