{"doi":"10.1145/3584371.3612948","title":"A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and Maintainability","abstract":"Rapid advancements in structural bioinformatics result in short software lifespans due to issues with scalability, portability and maintainability. In many cases, researchers aim to distribute scientific software as part of a research project but lack the development resources to maintain a robust web application server. Here, we introduce a web application framework and example that takes advantage of containers and the virtualization capabilities associated with them, and present an example application as a template. We contain the full web application in a container, which packages all the code and dependencies required for the software. The application itself is built specifically for structural bioinformatics, with a front end GUI and molecular viewer as well as a back end that can be altered to run arbitrary software tools. The container, which is a snapshot of the software, limits the effort required for porting and maintaining the software. At the same time, the architecture we introduce streamlines the process of starting a web server for programmers that are not web developers. Finally, for computationally intensive work, the container transfers computing costs to users in a pay-as-you-use model. An example of the web application implementation built in a container can be found in section 5.","journal":null,"year":2023,"id":397431,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9502,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1173266,"name":"Alexandra Chua","orcid":"0009-0009-1352-5264","position":1,"is_corresponding":false},{"id":1173267,"name":"Adyn Gallagher","orcid":"0009-0004-5509-2130","position":2,"is_corresponding":false},{"id":1173268,"name":"Denice Omene","orcid":"0009-0006-1952-7269","position":3,"is_corresponding":false},{"id":1173269,"name":"Danielle Okun","orcid":"0009-0005-3032-7076","position":4,"is_corresponding":false},{"id":1173270,"name":"Dominic DiFranzo","orcid":"0000-0001-6039-1806","position":5,"is_corresponding":false},{"id":531857,"name":"Brian Y. Chen","orcid":"0000-0001-9025-0107","position":6,"is_corresponding":false},{"id":877776,"name":"Justin Z. Tam","orcid":"0000-0003-3280-7397","position":0,"is_corresponding":true}],"reference_count":6,"raw_metadata":null,"created_at":"2026-07-19T01:19:39.497368Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}