Software
"Software" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus,
MeSH (Medical Subject Headings). Descriptors are arranged in a hierarchical structure,
which enables searching at various levels of specificity.
Sequential operating instructions for a particular problem or function to be run on a digital computer.
Descriptor ID |
D012984
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MeSH Number(s) |
L01.224.900
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Concept/Terms |
Software- Software
- Computer Software
- Software, Computer
- Computer Programs
- Computer Program
- Program, Computer
- Programs, Computer
Software Tools- Software Tools
- Software Tool
- Tool, Software
- Tools, Software
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Below are MeSH descriptors whose meaning is more general than "Software".
Below are MeSH descriptors whose meaning is more specific than "Software".
This graph shows the total number of publications written about "Software" by people in UAMS Profiles by year, and whether "Software" was a major or minor topic of these publications.
To see the data from this visualization as text, click here.
Year | Major Topic | Minor Topic | Total |
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2025 | 2 | 1 | 3 | 2024 | 0 | 2 | 2 | 2023 | 3 | 3 | 6 | 2022 | 0 | 2 | 2 | 2021 | 2 | 5 | 7 | 2020 | 6 | 3 | 9 | 2019 | 2 | 1 | 3 | 2018 | 2 | 3 | 5 | 2017 | 3 | 2 | 5 | 2016 | 4 | 4 | 8 | 2015 | 2 | 5 | 7 | 2014 | 4 | 9 | 13 | 2013 | 3 | 8 | 11 | 2012 | 2 | 2 | 4 | 2011 | 1 | 3 | 4 | 2010 | 2 | 1 | 3 | 2009 | 2 | 2 | 4 | 2008 | 3 | 6 | 9 | 2007 | 4 | 4 | 8 | 2006 | 0 | 2 | 2 | 2004 | 1 | 2 | 3 | 2003 | 0 | 1 | 1 | 2002 | 1 | 1 | 2 | 2000 | 1 | 0 | 1 | 1998 | 0 | 1 | 1 | 1995 | 1 | 1 | 2 | 1992 | 0 | 2 | 2 | 1990 | 0 | 1 | 1 |
To return to the timeline, click here.
Below are the most recent publications written about "Software" by people in Profiles over the past ten years.
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Lu D, Kalantar KL, Glascock AL, Chu VT, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform. Genome Med. 2025 May 06; 17(1):46.
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Wang T, Tam J, Chum T, Tai C, Marshall DC, Buckstein M, Liu J, Green S, Stewart RD, Liu T, Chao M. Evaluation of AI-based auto-contouring tools in radiotherapy: A single-institution study. J Appl Clin Med Phys. 2025 Apr; 26(4):e14620.
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Du X, Dobrowolski A, Brochhausen M, Garrett TJ, Hogan WR, Lemas DJ. Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing. J Am Soc Mass Spectrom. 2025 Feb 05; 36(2):433-438.
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O'Connell KA, Kopchick B, Carlson T, Belardo D, Byrum SD. Understanding proteome quantification in an interactive learning module on Google Cloud Platform. Brief Bioinform. 2024 Jul 23; 25(Supplement_1).
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McAfee L, Heath Z, Anderson W, Hozi M, Orr JW, Kang YA. The development of an automated microscope image tracking and analysis system. Biotechnol Prog. 2024 Nov-Dec; 40(6):e3490.
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Lemas DJ, Du X, Rouhizadeh M, Lewis B, Frank S, Wright L, Spirache A, Gonzalez L, Cheves R, Magalh?es M, Zapata R, Reddy R, Xu K, Parker L, Harle C, Young B, Louis-Jaques A, Zhang B, Thompson L, Hogan WR, Modave F. Classifying early infant feeding status from clinical notes using natural language processing and machine learning. Sci Rep. 2024 04 03; 14(1):7831.
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Charrasse S, Racine V, Saint-Omer C, Poquillon T, Lionnard L, Ledru M, Gonindard C, Delaunois S, Kissa K, Frye RE, Pastore M, Reynes C, Frechet M, Chajra H, Aouacheria A. Quantitative imaging and semiotic phenotyping of mitochondrial network morphology in live human cells. PLoS One. 2024; 19(3):e0301372.
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Chappell K, Byrum SD. Understanding PTM Cross Talk Through a Visualization Tool, PTMViz. Methods Mol Biol. 2024; 2836:57-65.
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Buatti JS, Kirby N, Stathakis S, Li R, Sivabhaskar S, de Oliveira M, Duke K, Kabat CN, Papanikolaou N, Paragios N. Standardizing and improving dose predictions for head and neck cancers using complete sets of OAR contours. Med Phys. 2024 Feb; 51(2):898-909.
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Ryan ML, Knod JL, Pandya SR. Creation of Three-dimensional Anatomic Models in Pediatric Surgical Patients Using Cross-sectional Imaging: A Demonstration of Low-cost Methods and Applications. J Pediatr Surg. 2024 Mar; 59(3):426-431.
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Du X, Dastmalchi F, Diller MA, Brochhausen M, Garrett TJ, Hogan WR, Lemas DJ. An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing. J Am Soc Mass Spectrom. 2023 Dec 06; 34(12):2857-2863.
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Shafi O, Liu D, Thompson C, Margo T, Bennett T, Suresh S, Yu F. Defining Electronic Health Record Standards for Child Health: A State-of-the-Art Review. Appl Clin Inform. 2024 01; 15(1):55-63.
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Eisenstein EL, Zozus MN, Garza MY, Lanham HJ, Adagarla B, Walden A, Benjamin DK, Zimmerman KO, Kumar KR. Assessing clinical site readiness for electronic health record (EHR)-to-electronic data capture (EDC) automated data collection. Contemp Clin Trials. 2023 05; 128:107144.
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Du X, Dastmalchi F, Ye H, Garrett TJ, Diller MA, Liu M, Hogan WR, Brochhausen M, Lemas DJ. Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software. Metabolomics. 2023 02 06; 19(2):11.
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Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database (Oxford). 2022 10 08; 2022.
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Steiner SM, Slavych BK, Zraick RI. Assessment of Online Patient Education Material About Dysphagia. Dysphagia. 2023 06; 38(3):990-1000.
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Shekar P V, Vignesh Rangaswamy V, Subramanian M, Atreya AR, Yalagudri S, Chennapragada S, Saggu DK, Narasimhan C. High rate episodes in a dual chamber pacemaker: What is the mechanism? Pacing Clin Electrophysiol. 2022 Feb; 45(2):238-240.
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Robeson MS, O'Rourke DR, Kaehler BD, Ziemski M, Dillon MR, Foster JT, Bokulich NA. RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comput Biol. 2021 11; 17(11):e1009581.
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West AP, Wertheim JO, Wang JC, Vasylyeva TI, Havens JL, Chowdhury MA, Gonzalez E, Fang CE, Di Lonardo SS, Hughes S, Rakeman JL, Lee HH, Barnes CO, Gnanapragasam PNP, Yang Z, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Nat Commun. 2021 08 09; 12(1):4886.
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Jarugula P, Scott S, Ivaturi V, Noack A, Moffett BS, Bhutta A, Gobburu JVS. Understanding the Role of Pharmacometrics-Based Clinical Decision Support Systems in Pediatric Patient Management: A Case Study Using Lyv Software. J Clin Pharmacol. 2021 06; 61 Suppl 1:S125-S132.
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Siebert JC, Saint-Cyr M, Borengasser SJ, Wagner BD, Lozupone CA, G?rg C. CANTARE: finding and visualizing network-based multi-omic predictive models. BMC Bioinformatics. 2021 Feb 19; 22(1):80.
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Wardell CP, Ashby C, Bauer MA. FiNGS: high quality somatic mutations using filters for next generation sequencing. BMC Bioinformatics. 2021 Feb 18; 22(1):77.
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Kulbeth HJ, Fukuda S, Brents LK. Automated quantification of opioid withdrawal in neonatal rat pups using Ethovision? XT software. Neurotoxicol Teratol. 2021 Mar-Apr; 84:106959.
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Jenjaroenpun P, Wongsurawat T, Wadley TD, Wassenaar TM, Liu J, Dai Q, Wanchai V, Akel NS, Jamshidi-Parsian A, Franco AT, Boysen G, Jennings ML, Ussery DW, He C, Nookaew I. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res. 2021 01 25; 49(2):e7.
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Yang X, Bian J, Hogan WR, Wu Y. Clinical concept extraction using transformers. J Am Med Inform Assoc. 2020 12 09; 27(12):1935-1942.
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Patel L, Shukla T, Huang X, Ussery DW, Wang S. Machine Learning Methods in Drug Discovery. Molecules. 2020 Nov 12; 25(22).
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Price NB, Chizinski CJ, Fontaine JJ, Pope KL, Rahe M, Rawlinson J. An open-sourced, web-based application to improve our ability to understand hunter and angler purchasing behavior from license data. PLoS One. 2020; 15(10):e0226397.
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Licon AL, Alexandrian A, Saenz D, Myers P, Rasmussen K, Stathakis S, Papanikolaou N, Kirby N. An open-source tool to visualize potential cone collisions while planning SRS cases. J Appl Clin Med Phys. 2020 Oct; 21(10):40-47.
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Drew ED, Janes RW. PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures. Nucleic Acids Res. 2020 07 02; 48(W1):W17-W24.
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Soong D, Stratford J, Avet-Loiseau H, Bahlis N, Davies F, Dispenzieri A, Sasser AK, Schecter JM, Qi M, Brown C, Jones W, Keats JJ, Auclair D, Chiu C, Powers J, Schaffer M. CNV Radar: an improved method for somatic copy number alteration characterization in oncology. BMC Bioinformatics. 2020 Mar 06; 21(1):98.
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Zhang Y, Koru G. Understanding and detecting defects in healthcare administration data: Toward higher data quality to better support healthcare operations and decisions. J Am Med Inform Assoc. 2020 03 01; 27(3):386-395.
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Caputo M, Lyles JT, Salazar MS, Quave CL. LEGO MINDSTORMS Fraction Collector: A Low-Cost Tool for a Preparative High-Performance Liquid Chromatography System. Anal Chem. 2020 01 21; 92(2):1687-1690.
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Grigorian A, Fang P, Kirk T, Efendizade A, Jadidi J, Sighary M, Cohen-Addad DI. Learning from Gamers: Integrating Alternative Input Devices and AutoHotkey Scripts to Simplify Repetitive Tasks and Improve Workflow. Radiographics. 2020 Jan-Feb; 40(1):141-150.
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Cooke MB, O'Leary TP, Harris P, Ma R, Brown RE, Snyder JS. Pathfinder: open source software for analyzing spatial navigation search strategies. F1000Res. 2019; 8:1521.
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Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodr?guez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, V?zquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857.
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Bathla G, Limaye K, Policeni B, Klotz E, Juergens M, Derdeyn C. Achieving comparable perfusion results across vendors. The next step in standardizing stroke care: a technical report. J Neurointerv Surg. 2019 Dec; 11(12):1257-1260.
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Long DE, Villasante Tezanos AG, Wise JN, Kern PA, Bamman MM, Peterson CA, Dennis RA. A guide for using NIH Image J for single slice cross-sectional area and composition analysis of the thigh from computed tomography. PLoS One. 2019; 14(2):e0211629.
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Kuo PH, Eshghi N, Tinaz S, Blumenfeld H, Louis ED, Zubal G. Optimization of Parameters for Quantitative Analysis of 123I-Ioflupane SPECT Images for Monitoring Progression of Parkinson Disease. J Nucl Med Technol. 2019 Mar; 47(1):70-74.
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Lossio-Ventura JA, Hogan W, Modave F, Guo Y, He Z, Yang X, Zhang H, Bian J. OC-2-KB: integrating crowdsourcing into an obesity and cancer knowledge base curation system. BMC Med Inform Decis Mak. 2018 07 23; 18(Suppl 2):55.
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McCarty JL, Golofit P, Tigges S, Skalski M. Digital Medical Illustration for the Radiologist. Radiographics. 2018 Jul-Aug; 38(4):1145-1157.
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Younes F, Cosyn J, De Bruyckere T, Cleymaet R, Bouckaert E, Eghbali A. A randomized controlled study on the accuracy of free-handed, pilot-drill guided and fully guided implant surgery in partially edentulous patients. J Clin Periodontol. 2018 06; 45(6):721-732.
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Tuazon B, Narayanasamy G, Papanikolaou N, Kirby N, Mavroidis P, Stathakis S. Evaluation and comparison of second-check monitor unit calculation software with Pinnacle3 treatment planning system. Phys Med. 2018 Jan; 45:186-191.
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Dobretsov M, Petkau G, Hayar A, Petkau E. Clock Scan Protocol for Image Analysis: ImageJ Plugins. J Vis Exp. 2017 06 19; (124).
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Scanlon DP, Bah A, Krzeminski M, Zhang W, Leduc-Pessah HL, Dong YN, Forman-Kay JD, Salter MW. An evolutionary switch in ND2 enables Src kinase regulation of NMDA receptors. Nat Commun. 2017 05 16; 8:15220.
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Pedersen TL, Nookaew I, Wayne Ussery D, M?nsson M. PanViz: interactive visualization of the structure of functionally annotated pangenomes. Bioinformatics. 2017 04 01; 33(7):1081-1082.
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Thankaswamy-Kosalai S, Sen P, Nookaew I. Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. Genomics. 2017 07; 109(3-4):186-191.
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Hogan WR, Hanna J, Hicks A, Amirova S, Bramblett B, Diller M, Enderez R, Modzelewski T, Vasconcelos M, Delcher C. Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request. J Biomed Semantics. 2017 Mar 03; 8(1):10.
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Zheng J, Erzurumluoglu AM, Elsworth BL, Kemp JP, Howe L, Haycock PC, Hemani G, Tansey K, Laurin C, Pourcain BS, Warrington NM, Finucane HK, Price AL, Bulik-Sullivan BK, Anttila V, Paternoster L, Gaunt TR, Evans DM, Neale BM. LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics. 2017 01 15; 33(2):272-279.
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Mavridis L, Janes RW. PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates. Bioinformatics. 2017 01 01; 33(1):56-63.
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Whitmore L, Miles AJ, Mavridis L, Janes RW, Wallace BA. PCDDB: new developments at the Protein Circular Dichroism Data Bank. Nucleic Acids Res. 2017 01 04; 45(D1):D303-D307.
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Hogan WR, Wagner MM, Brochhausen M, Levander J, Brown ST, Millett N, DePasse J, Hanna J. The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. J Biomed Semantics. 2016 Aug 18; 7:50.
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Kirkwood ML, Guild JB, Arbique GM, Tsai S, Modrall JG, Anderson JA, Rectenwald J, Timaran C. New image-processing and noise-reduction software reduces radiation dose during complex endovascular procedures. J Vasc Surg. 2016 Nov; 64(5):1357-1365.
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Stupnikov A, Tripathi S, de Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F. samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. 2016 11 01; 32(21):3345-3347.
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Gillies CE, Otto EA, Vega-Warner V, Robertson CC, Sanna-Cherchi S, Gharavi A, Crawford B, Bhimma R, Winkler C, Kang HM, Sampson MG. tarSVM: Improving the accuracy of variant calls derived from microfluidic PCR-based targeted next generation sequencing using a support vector machine. BMC Bioinformatics. 2016 Jun 10; 17(1):233.
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Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS One. 2016; 11(4):e0154556.
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Shibata A, Okuno T, Rahman MA, Azuma Y, Takeda J, Masuda A, Selcen D, Engel AG, Ohno K. IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome. J Hum Genet. 2016 Jul; 61(7):633-40.
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Pokhrel D, McClinton C, Sood S, Badkul R, Saleh H, Jiang H, Lominska C. Monte Carlo evaluation of tissue heterogeneities corrections in the treatment of head and neck cancer patients using stereotactic radiotherapy. J Appl Clin Med Phys. 2016 03 08; 17(2):258-270.
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Leroux S, Turner MA, Guellec CB, Hill H, van den Anker JN, Kearns GL, Jacqz-Aigrain E, Zhao W. Pharmacokinetic Studies in Neonates: The Utility of an Opportunistic Sampling Design. Clin Pharmacokinet. 2015 Dec; 54(12):1273-85.
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La Rosa PS, Brooks TL, Deych E, Shands B, Prior F, Larson-Prior LJ, Shannon WD. Gibbs distribution for statistical analysis of graphical data with a sample application to fcMRI brain images. Stat Med. 2016 Feb 20; 35(4):566-80.
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Choudhri AF, Chatterjee AR, Javan R, Radvany MG, Shih G. Security Issues for Mobile Medical Imaging: A Primer. Radiographics. 2015 Oct; 35(6):1814-24.
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