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{ "count": 29616, "next": "?page=2", "previous": null, "list": [ { "name": "CellDialog", "description": "Computational framework for ligand-receptor-mediated cell-cell communication analysis III.", "homepage": "https://github.com/plhhnu/CellDialog", "biotoolsID": "celldialog", "biotoolsCURIE": "biotools:celldialog", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3937", "term": "Feature extraction" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1109/JBHI.2023.3333828", "pmid": "37976192", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "CellDialog: A Computational Framework for Ligand-Receptor-Mediated Cell-Cell Communication Analysis", "abstract": "Intercellularcommunication significantly influences tumor progression, metastasis, and therapy resistance. An intercellular communication inference method includes two main procedures: ligand-receptor interaction (LRI) curation and LRI-mediated intercellular communication strength measurement. The construction of a comprehensive, high-confident and well-organized LRI database contributes to intercellular communication inference. Here, we developed a computational framework named CellDialog to reconstruct an intercellular connectivity network based on the combined expression of ligands and receptors involved in sender and receiver cells. CellDialog first captures high-confident LRIs through LRI feature extraction, feature selection, and classification. Furthermore, CellDialog uses a three-point estimation approach to measure the LRI-mediated intercellular communication strength by combining LRI filtering and single-cell RNA sequencing data. A comparison analysis of CellDialog and the other tools was conducted, and it was found that CellDialog can efficiently decode intercellular communications. Additionally, CellDialog offers a heatmap view and network view for intercellular communication visualization. In summary, CellDialog provides a tool that allows researchers to analyze intercellular signal transduction.", "date": "2024-01-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Peng L." }, { "name": "Xiong W." }, { "name": "Han C." }, { "name": "Li Z." }, { "name": "Chen X." } ], "journal": "IEEE Journal of Biomedical and Health Informatics" } } ], "credit": [ { "name": "Lihong Peng", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-01T09:12:32.628028Z", "lastUpdate": "2024-05-01T09:12:32.630915Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Mesoscope", "description": "Mesoscope is a web-based data integration and curation tool. Mesoscope allows users to begin with a listing of molecules (such as data from proteomics), and to use resources at UniProt and the PDB to identify, prepare and validate appropriate structures and representations for each molecule, ultimately producing a portable output file used by CellPACK and other modeling tools for generation of 3D models of the biological mesoscale.", "homepage": "http://mesoscope.scripps.edu/beta", "biotoolsID": "mesoscope", "biotoolsCURIE": "biotools:mesoscope", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3452", "term": "Tomography" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.2312/MOLVA.20201098", "pmid": "37928321", "pmcid": "PMC10624244", "type": [], "version": null, "note": null, "metadata": { "title": "Mesoscope: AWeb-based Tool for Mesoscale Data Integration and Curation", "abstract": "Interest is growing for 3D models of the biological mesoscale, the intermediate scale between the nanometer scale of molecular structure and micrometer scale of cellular biology. However, it is currently difficult to gather, curate and integrate all the data required to define such models. To address this challenge we developed Mesoscope (mesoscope.scripps.edu/beta), a web-based data integration and curation tool. Mesoscope allows users to begin with a listing of molecules (such as data from proteomics), and to use resources at UniProt and the PDB to identify, prepare and validate appropriate structures and representations for each molecule, ultimately producing a portable output file used by CellPACK and other modeling tools for generation of 3D models of the biological mesoscale. The availability of this tool has proven essential in several exploratory applications, given the high complexity of mesoscale models and the heterogeneity of the available data sources.", "date": "2020-01-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Autin L." }, { "name": "Maritan M." }, { "name": "Barbaro B.A." }, { "name": "Gardner A." }, { "name": "Olson A.J." }, { "name": "Sanner M." }, { "name": "Goodsell D.S." } ], "journal": "MolVA 2020 - Workshop on Molecular Graphics and Visual Analysis of Molecular Data" } } ], "credit": [ { "name": "L Autin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "D S Goodsell", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-01T09:09:56.514175Z", "lastUpdate": "2024-05-01T09:09:56.516367Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PLM-ARG", "description": "Antibiotic resistance gene identification using a pretrained protein language model.", "homepage": "http://www.unimd.org/PLM-ARG", "biotoolsID": "plm-arg", "biotoolsCURIE": "biotools:plm-arg", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3482", "term": "Antimicrobial resistance prediction" }, { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3941", "term": "Metatranscriptomics" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Junwu302/PLM-ARG", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAD690", "pmid": "37995287", "pmcid": "PMC10676515", "type": [], "version": null, "note": null, "metadata": { "title": "PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model", "abstract": "Motivation: Antibiotic resistance presents a formidable global challenge to public health and the environment. While considerable endeavors have been dedicated to identify antibiotic resistance genes (ARGs) for assessing the threat of antibiotic resistance, recent extensive investigations using metagenomic and metatranscriptomic approaches have unveiled a noteworthy concern. A significant fraction of proteins defies annotation through conventional sequence similarity-based methods, an issue that extends to ARGs, potentially leading to their under-recognition due to dissimilarities at the sequence level. Results: Herein, we proposed an Artificial Intelligence-powered ARG identification framework using a pretrained large protein language model, enabling ARG identification and resistance category classification simultaneously. The proposed PLM-ARG was developed based on the most comprehensive ARG and related resistance category information (>28K ARGs and associated 29 resistance categories), yielding Matthew's correlation coefficients (MCCs) of 0.983 ± 0.001 by using a 5-fold cross-validation strategy. Furthermore, the PLM-ARG model was verified using an independent validation set and achieved an MCC of 0.838, outperforming other publicly available ARG prediction tools with an improvement range of 51.8%-107.9%. Moreover, the utility of the proposed PLM-ARG model was demonstrated by annotating resistance in the UniProt database and evaluating the impact of ARGs on the Earth's environmental microbiota.", "date": "2023-11-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Wu J." }, { "name": "Ouyang J." }, { "name": "Qin H." }, { "name": "Zhou J." }, { "name": "Roberts R." }, { "name": "Siam R." }, { "name": "Wang L." }, { "name": "Tong W." }, { "name": "Liu Z." }, { "name": "Shi T." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Weida Tong", "email": "weida.tong@fda.hhs.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Zhichao Liu", "email": "zhichao.liu@boehringer-ingelheim.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Tieliu Shi", "email": "tlshi@bio.ecnu.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-01T09:07:33.334601Z", "lastUpdate": "2024-05-01T09:07:33.336652Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "AFRbase", "description": "Database of protein mutations responsible for antifungal resistance.", "homepage": "http://proteininformatics.org/mkumar/afrbase/", "biotoolsID": "afrbase", "biotoolsCURIE": "biotools:afrbase", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAD677", "pmid": "37947313", "pmcid": "PMC10656092", "type": [], "version": null, "note": null, "metadata": { "title": "AFRbase: a database of protein mutations responsible for antifungal resistance", "abstract": "Motivation: Fungal pathogens are known to cause life threatening invasive infections with rising global mortality rates. Besides, the indiscriminate use of antifungals in both clinics and agriculture has promoted antifungal drug resistance in the last decade. Fungi can show drug resistance by a variety of mechanisms. But primary driver in all these hitherto documented mechanisms is stable and heritable point mutations in the key proteins. Therefore, cataloguing mutations that can confer resistance is the first step toward understanding the mechanisms leading to the emergence of antifungal resistance. Results: In the present, work we have described a database of all the mutations responsible for antifungal resistance. Named as antifungal resistance database (AFRbase), it is better than the existing databases of antifungal resistance namely, FunResDB and MARDy which have a limited scope and inadequate information. Data of AFRbase was collected using both text mining and manual curation. AFRbase provides a separate window for visualization of mutations in the 2D and 3D formats making it easy for researchers to analyze the mutation data and ensures interoperability with other standard molecular biology databases like NCBI and UniProtKB. We hope AFRbase can be useful to both clinicians and basic biomedical scientists as we envision it as an important resource for genotypic susceptibility testing of fungi and to study/predict the course of evolution of antifungal resistance. The current version of AFRbase contains manually curated 3691 unique mutations present in 29 proteins of 32 fungal species along with the information of drugs against which resistance is caused.", "date": "2023-11-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Jain A." }, { "name": "Singhal N." }, { "name": "Kumar M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Manish Kumar", "email": "manish@south.du.ac.in", "url": null, "orcidid": "https://orcid.org/0000-0002-7936-9892", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Antonio Pedro Camargo", "email": "antoniop.camargo@lbl.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-01T09:04:12.913221Z", "lastUpdate": "2024-05-01T09:04:12.915997Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "VirusHound-I", "description": "Prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation.", "homepage": "https://www.biochemintelli.com/VirusHound-I", "biotoolsID": "virushound-i", "biotoolsCURIE": "biotools:virushound-i", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3461", "term": "Virulence prediction" }, { "uri": "http://edamontology.org/operation_0252", "term": "Peptide immunogenicity prediction" }, { "uri": "http://edamontology.org/operation_0416", "term": "Epitope mapping" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3948", "term": "Immunoinformatics" }, { "uri": "http://edamontology.org/topic_3930", "term": "Immunogenetics" }, { "uri": "http://edamontology.org/topic_2830", "term": "Immunoproteins and antigens" }, { "uri": "http://edamontology.org/topic_0202", "term": "Pharmacology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/jfbldevs/virushound-I", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIB/BBAD434", "pmid": "38033292", "pmcid": "PMC10753651", "type": [], "version": null, "note": null, "metadata": { "title": "VirusHound-I: prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation", "abstract": "Throughout evolution, pathogenic viruses have developed different strategies to evade the response of the adaptive immune system. To carry out successful replication, some pathogenic viruses encode different proteins that manipulate the molecular mechanisms of host cells. Currently, there are different bioinformatics tools for virus research; however, none of them focus on predicting viral proteins that evade the adaptive system. In this work, we have developed a novel tool based on machine and deep learning for predicting this type of viral protein named VirusHound-I. This tool is based on a model developed with the multilayer perceptron algorithm using the dipeptide composition molecular descriptor. In this study, we have also demonstrated the robustness of our strategy for data augmentation of the positive dataset based on generative antagonistic networks. During the 10-fold cross-validation step in the training dataset, the predictive model showed 0.947 accuracy, 0.994 precision, 0.943 F1 score, 0.995 specificity, 0.896 sensitivity, 0.894 kappa, 0.898 Matthew’s correlation coefficient and 0.989 AUC. On the other hand, during the testing step, the model showed 0.964 accuracy, 1.0 precision, 0.967 F1 score, 1.0 specificity, 0.936 sensitivity, 0.929 kappa, 0.931 Matthew’s correlation coefficient and 1.0 AUC. Taking this model into account, we have developed a tool called VirusHound-I that makes it possible to predict viral proteins that evade the host’s adaptive immune system. We believe that VirusHound-I can be very useful in accelerating studies on the molecular mechanisms of evasion of pathogenic viruses, as well as in the discovery of therapeutic targets.", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Beltran J.F." }, { "name": "Belen L.H." }, { "name": "Farias J.G." }, { "name": "Zamorano M." }, { "name": "Lefin N." }, { "name": "Miranda J." }, { "name": "Parraguez-Contreras F." } ], "journal": "Briefings in Bioinformatics" } } ], "credit": [ { "name": "Jorge F Beltrán", "email": "beltran.lissabet.jf@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-2703-9629", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Fernanda Parraguez-Contreras", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-30T13:12:13.495572Z", "lastUpdate": "2024-04-30T13:12:13.499807Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "JSONWP", "description": "Static website generator for protein bioinformatics research.\n\nIt is a JS application that creates a website based on the JSON data.", "homepage": "http://jsonwp.onrender.com", "biotoolsID": "jsonwp", "biotoolsCURIE": "biotools:jsonwp", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3372", "term": "Software engineering" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "JavaScript" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/MesihK/react-json-wpbuilder", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOADV/VBAD154", "pmid": "37904893", "pmcid": "PMC10613403", "type": [], "version": null, "note": null, "metadata": { "title": "JSONWP: a static website generator for protein bioinformatics research", "abstract": "Motivation: Presenting the integrated results of bioinformatics research can be challenging and requires sophisticated visualization components, which can be time-consuming to develop. This article presents a new way to effectively communicate research findings. Results: We have developed a static web page generator, JSONWP, which is specifically designed for protein bioinformatics research. Utilizing React (a JavaScript library used to build interactive and dynamic user interfaces for web applications), we have integrated publicly available bioinformatics visualization components to provide standardized access to these components. JSON (or JavaScript Object Notation, is a lightweight textual data format often used to structure and exchange information between different software tools.) is used as the input source due to its ability to represent nearly all types of data using key and value pairs. This allows researchers to use their preferred programming language to create a JSON representation, which can then be converted into a website by JSONWP. No server or domain is required to host the website, as only the publicly accessible JSON file is required. Conclusions: Overall, JSONWP provides a useful new tool for bioinformatics researchers to effectively communicate their findings. The open-source implementation is located at https://github.com/MesihK/react-json-wpbuilder, and the tool can be used at jsonwp.onrender.com.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Kilinc M." }, { "name": "Jia K." }, { "name": "Jernigan R.L." } ], "journal": "Bioinformatics Advances" } } ], "credit": [ { "name": "Robert L Jernigan", "email": "jernigan@iastate.edu", "url": null, "orcidid": "https://orcid.org/0000-0003-0996-8360", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Mesih Kilinc", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-30T13:03:54.037389Z", "lastUpdate": "2024-04-30T13:03:54.039616Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Cell4D", "description": "Cell4D is a Linux C++-based graphical spatial stochatic cell simulator capable of simulating a wide variety of cellular pathways. Molecules are simulated as particles within a user-defined simulation space under a Smoluchowski-based reaction-diffusion system on a static time-step basis.", "homepage": "https://github.com/ParkinsonLab/cell4d", "biotoolsID": "cell4d", "biotoolsCURIE": "biotools:cell4d", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3928", "term": "Pathway analysis" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" } ], "operatingSystem": [], "language": [ "C++" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-024-05739-0", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Cell4D: a general purpose spatial stochastic simulator for cellular pathways", "abstract": "Background: With the generation of vast compendia of biological datasets, the challenge is how best to interpret ‘omics data alongside biochemical and other small-scale experiments to gain meaningful biological insights. Key to this challenge are computational methods that enable domain-users to generate novel hypotheses that can be used to guide future experiments. Of particular interest are flexible modeling platforms, capable of simulating a diverse range of biological systems with low barriers of adoption to those with limited computational expertise. Results: We introduce Cell4D, a spatial-temporal modeling platform combining a robust simulation engine with integrated graphics visualization, a model design editor, and an underlying XML data model capable of capturing a variety of cellular functions. Cell4D provides an interactive visualization mode, allowing intuitive feedback on model behavior and exploration of novel hypotheses, together with a non-graphics mode, compatible with high performance cloud compute solutions, to facilitate generation of statistical data. To demonstrate the flexibility and effectiveness of Cell4D, we investigate the dynamics of CEACAM1 localization in T-cell activation. We confirm the importance of Ca2+ microdomains in activating calmodulin and highlight a key role of activated calmodulin on the surface expression of CEACAM1. We further show how lymphocyte-specific protein tyrosine kinase can help regulate this cell surface expression and exploit spatial modeling features of Cell4D to test the hypothesis that lipid rafts regulate clustering of CEACAM1 to promote trans-binding to neighbouring cells. Conclusions: Through demonstrating its ability to test and generate hypotheses, Cell4D represents an effective tool to help integrate knowledge across diverse, large and small-scale datasets.", "date": "2024-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Chan D." }, { "name": "Cromar G.L." }, { "name": "Taj B." }, { "name": "Parkinson J." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "John Parkinson", "email": "jparkin@sickkids.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Donny Chan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-30T12:45:47.267049Z", "lastUpdate": "2024-04-30T12:45:47.269277Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "JeasyTFM", "description": "Open-source software package for the analysis of large 2D TFM data within ImageJ.", "homepage": "http://questpharma.u-strasbg.fr/JEasyTFM.html", "biotoolsID": "jeasytfm", "biotoolsCURIE": "biotools:jeasytfm", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3934", "term": "Cytometry" }, { "uri": "http://edamontology.org/topic_3318", "term": "Physics" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://questpharma.u-strasbg.fr/JEasyTFM_manual.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOADV/VBAD156", "pmid": "37928344", "pmcid": "PMC10625472", "type": [], "version": null, "note": null, "metadata": { "title": "JEasyTFM: an open-source software package for the analysis of large 2D TFM data within ImageJ", "abstract": "Motivation: Cells adhering to the extracellular matrix can sense and respond to a wide variety of chemical and physical features of the adhesive surface. Traction force microscopy (TFM) allows determining the tensile forces exerted by the cells on their substrate with high resolution. Results: To allow broad access of this techniques to cell biology laboratories we developed JeasyTFM, an open-source ImageJ package able to process multi-color and multi-position time-lapse pictures thus suitable for the automatic analysis of large TFM data.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Carl P." }, { "name": "Ronde P." } ], "journal": "Bioinformatics Advances" } } ], "credit": [ { "name": "Philippe Carl", "email": "philippe.carl@unistra.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-8063-3294", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Philippe Rondé", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-30T12:35:46.193814Z", "lastUpdate": "2024-04-30T12:35:46.196223Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "syntenyPlotteR", "description": "User-friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians.", "homepage": "https://farre-lab.github.io/syntenyPlotteR/", "biotoolsID": "syntenyplotter", "biotoolsCURIE": "biotools:syntenyplotter", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" }, { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOADV/VBAD161", "pmid": "38023328", "pmcid": "PMC10660287", "type": [], "version": null, "note": null, "metadata": { "title": "syntenyPlotteR: a user-friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians", "abstract": "Motivation: The rapid increase in the number of chromosome-scale genome assemblies has renewed interest in chromosome evolution studies. The visualization of syntenic relationships between genomes is a crucial initial step in the study of chromosome rearrangements and evolution. There are few tools available that serve this purpose, and they can be difficult to learn. Moreover, these tools are limited in the number of species comparisons that can be visualized and the size of chromosome rearrangements identified. Thus, the development of novel visualization tools is in strong need. Results: Here, we present syntenyPlotteR, an R package developed to visualize homologous synteny blocks in a pairwise or multispecies manner. This package contains three functions that allow users to generate publication-quality representations of syntenic relationships easily and quickly between genomes of interest.", "date": "2023-01-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Quigley S." }, { "name": "Damas J." }, { "name": "Larkin D.M." }, { "name": "Farre M." } ], "journal": "Bioinformatics Advances" } } ], "credit": [ { "name": "Marta Farré", "email": "m.farre-belmonte@kent.ac.uk", "url": null, "orcidid": "https://orcid.org/0000-0001-9170-5767", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sarah Quigley", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-30T12:33:30.345341Z", "lastUpdate": "2024-04-30T12:33:30.347736Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DegronMD", "description": "DegronMD: protein-targeted degradation, mutation and drug response to degrons.", "homepage": "https://bioinfo.uth.edu/degronmd", "biotoolsID": "degronmd", "biotoolsCURIE": "biotools:degronmd", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_4009", "term": "Small molecule design" }, { "uri": "http://edamontology.org/operation_0417", "term": "PTM site prediction" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0140", "term": "Protein targeting and localisation" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/MOLBEV/MSAD253", "pmid": "37992195", "pmcid": "PMC10701100", "type": [], "version": null, "note": null, "metadata": { "title": "DegronMD: Leveraging Evolutionary and Structural Features for Deciphering Protein-Targeted Degradation, Mutations, and Drug Response to Degrons", "abstract": "Protein-Targeted degradation is an emerging and promising therapeutic approach. The specificity of degradation and the maintenance of cellular homeostasis are determined by the interactions between E3 ubiquitin ligase and degradation signals, known as degrons. The human genome encodes over 600 E3 ligases; however, only a small number of targeted degron instances have been identified so far. In this study, we introduced DegronMD, an open knowledgebase designed for the investigation of degrons, their associated dysfunctional events, and drug responses. We revealed that degrons are evolutionarily conserved and tend to occur near the sites of protein translational modifications, particularly in the regions of disordered structure and higher solvent accessibility. Through pattern recognition and machine learning techniques, we constructed the degrome landscape across the human proteome, yielding over 18,000 new degrons for targeted protein degradation. Furthermore, dysfunction of degrons disrupts the degradation process and leads to the abnormal accumulation of proteins; this process is associated with various types of human cancers. Based on the estimated phenotypic changes induced by somatic mutations, we systematically quantified and assessed the impact of mutations on degron function in pan-cancers; these results helped to build a global mutational map on human degrome, including 89,318 actionable mutations that may induce the dysfunction of degrons and disrupt protein degradation pathways. Multiomics integrative analysis unveiled over 400 drug resistance events associated with the mutations in functional degrons. DegronMD, accessible at https://bioinfo.uth.edu/degronmd, is a useful resource to explore the biological mechanisms, infer protein degradation, and assist with drug discovery and design on degrons.", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Xu H." }, { "name": "Hu R." }, { "name": "Zhao Z." } ], "journal": "Molecular Biology and Evolution" } } ], "credit": [ { "name": "Zhongming Zhao", "email": "zhongming.zhao@uth.tmc.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-3477-0914", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Haodong Xu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Ruifeng Hu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-30T12:31:41.312350Z", "lastUpdate": "2024-04-30T12:31:41.315403Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }