Dataset Information

Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy.

ABSTRACT: One aspect of personalized medicine is aiming at identifying specific targets for therapy considering the gene expression profile of each patient individually. The real-world implementation of this approach is better achieved by user-friendly bioinformatics systems for healthcare professionals. In this report, we present an online platform that endows users with an interface designed using MEAN stack supported by a Galaxy pipeline. This pipeline targets connection hubs in the subnetworks formed by the interactions between the proteins of genes that are up-regulated in tumors. This strategy has been proved to be suitable for the inhibition of tumor growth and metastasis in vitro. Therefore, Perl and Python scripts were enclosed in Galaxy for translating RNA-seq data into protein targets suitable for the chemotherapy of solid tumors. Consequently, we validated the process of target diagnosis by (i) reference to subnetwork entropy, (ii) the critical value of density probability of differential gene expression, and (iii) the inhibition of the most relevant targets according to TCGA and GDC data. Finally, the most relevant targets identified by the pipeline are stored in MongoDB and can be accessed through the aforementioned internet portal designed to be compatible with mobile or small devices through Angular libraries.

SUBMITTER: Pires JG

PROVIDER: S-EPMC7935533 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy.

Pires Jorge Guerra JG da Silva Gilberto Ferreira GF Weyssow Thomas T Conforte Alessandra Jordano AJ Pagnoncelli Dante D da Silva Fabricio Alves Barbosa FAB Carels Nicolas N

Frontiers in genetics 20210218

One aspect of personalized medicine is aiming at identifying specific targets for therapy considering the gene expression profile of each patient individually. The real-world implementation of this approach is better achieved by user-friendly bioinformatics systems for healthcare professionals. In this report, we present an online platform that endows users with an interface designed using MEAN stack supported by a Galaxy pipeline. This pipeline targets connection <i>hubs</i> in the subnetworks ...[more]

PMID: 33679888

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Project description:Computer-assisted drug design (CADD) methods have greatly contributed to the development of new drugs. Among CADD methodologies, virtual screening (VS) can enrich the compound collection with molecules that have the desired physicochemical and pharmacophoric characteristics that are needed to become drugs. Many free tools are available for this purpose, but they are difficult to use and do not have a graphical user interface. Furthermore, several free tools must be used to carry out the entire VS process, requiring the user to process the results of one software program so that they can be used in another program, adding a potential source of human error. Moreover, some software programs require knowledge of advanced computational skills, such as programming languages. This context has motivated us to develop Molecular Architect (MolAr). MolAr is a workflow with a simple and intuitive interface that acts in an integrated and automated form to perform the entire VS process, from protein preparation (homology modeling and protonation state) to virtual screening. MolAr carries out VS through AutoDock Vina, DOCK 6, or a consensus of the two. Two case studies were conducted to demonstrate the performance of MolAr. In the first study, the feasibility of using MolAr for DNA-ligand systems was assessed. Both AutoDock Vina and DOCK 6 showed good results in performing VS in DNA-ligand systems. However, the use of consensus virtual screening was able to enrich the results. According to the area under the ROC curve and the enrichment factors, consensus VS was better able to predict the positions of the active ligands. The second case study was performed on 8 targets from the DUD-E database and 10 active ligands for each target. The results demonstrated that using the final ligand conformation provided by AutoDock Vina as an input for DOCK 6 improved the DOCK 6 ROC curves by up to 42% in VS. These case studies demonstrated that MolAr is capable conducting the VS process and is an easy-to-use and effective tool. MolAr is available for download free of charge at http: //www.drugdiscovery.com.br/software/.

Project description:BackgroundHeterogeneity in the features, input-output behaviour and user interface for available bioinformatics tools and services is still a bottleneck for both expert and non-expert users. Advancement in providing common interfaces over such tools and services are gaining interest among researchers. However, the lack of (meta-) information about input-output data and parameter prevents to provide automated and standardized solutions, which can assist users in setting the appropriate parameters. These limitations must be resolved especially in the workflow-based solution in order to ease the integration of software.FindingsWe report a Taverna Workbench plugin: the XworX BIFI (Beautiful Interfaces for Inputs) implemented as a solution for the aforementioned issues. BIFI provides a Graphical User Interface (GUI) definition language used to layout the user interface and to define parameter options for Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF) directly or discover appropriate instances from a configured repository. In the absence of a GDF, BIFI generates a default interface.ConclusionThe Taverna Workbench is an open source software providing the ability to combine various services within a workflow. Nevertheless, users can supply input data to the workflow via a simple user interface providing only a text area to enter the input in text form. The workflow may contain meta-information in human readable form such as description text for the port and an example value. However, not all workflow ports are documented so well or have all the required information.BIFI uses custom user interface components for ports which give users feedback on the parameter data type or structure to be used for service execution and enables client-side data validations. Moreover, BIFI offers user interfaces that allow users to interactively construct workflow views and share them with the community, thus significantly increasing usability of heterogeneous, distributed service consumption.

Dataset Information

Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy.

Publications

Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy.

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