{"id":"https://openalex.org/W7225459042","doi":"https://doi.org/10.5281/zenodo.24026382","title":"Code for: Monotone and non-monotone pace along trajectories of nonlinear differential equations, with an application to the tempo of cell differentiation","display_name":"Code for: Monotone and non-monotone pace along trajectories of nonlinear differential equations, with an application to the tempo of cell differentiation","publication_year":2026,"publication_date":"2026-11-07","ids":{"openalex":"https://openalex.org/W7225459042","doi":"https://doi.org/10.5281/zenodo.24026382"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.24026382","doi":"https://doi.org/10.5281/zenodo.24026382","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.24026382","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"volume":null,"type":"software","is_traditional":false,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.24026382","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075064537","display_name":"Nobuo Okui","orcid":"https://orcid.org/0000-0001-5894-5283","observed_orcids":["https://orcid.org/0000-0001-5894-5283"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Okui, Nobuo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5075064537"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7939000129699707,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7939000129699707,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.12080000340938568,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.0038999998942017555,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pace-of-change","display_name":"pace of change","score":0.527999997138977},{"id":"https://openalex.org/keywords/nonlinear-differential-equations","display_name":"nonlinear differential equations","score":0.8299999833106995},{"id":"https://openalex.org/keywords/cell-differentiation","display_name":"cell differentiation","score":0.5329999923706055},{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"principal component analysis","score":0.5659999847412109},{"id":"https://openalex.org/keywords/bootstrap-confidence-intervals","display_name":"bootstrap confidence intervals","score":0.8610000014305115},{"id":"https://openalex.org/keywords/trajectory-analysis","display_name":"trajectory analysis","score":0.3149999976158142}],"concepts":[{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.6028000116348267},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.5403000116348267},{"id":"https://openalex.org/C2834757","wikidata":"https://www.wikidata.org/wiki/Q4925424","display_name":"Monotone polygon","level":2,"score":0.5259000062942505},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.511900007724762},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45879998803138733},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.45669999718666077},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4551999866962433},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4388999938964844},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.4323999881744385},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.3856000006198883},{"id":"https://openalex.org/C2780129039","wikidata":"https://www.wikidata.org/wiki/Q1931107","display_name":"Section (typography)","level":2,"score":0.3779999911785126},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.33640000224113464},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3091999888420105},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3043000102043152},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.2946999967098236},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.2825999855995178},{"id":"https://openalex.org/C2777686260","wikidata":"https://www.wikidata.org/wiki/Q144037","display_name":"Calculus (dental)","level":2,"score":0.2615000009536743}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.24026382","doi":"https://doi.org/10.5281/zenodo.24026382","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.24026382","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.24026383","doi":"https://doi.org/10.5281/zenodo.24026383","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.24026383","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.5281/zenodo.24026382","doi":"https://doi.org/10.5281/zenodo.24026382","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.24026382","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W6894116420","https://openalex.org/W6931324267","https://openalex.org/W6949974829","https://openalex.org/W7164840831","https://openalex.org/W6958855489","https://openalex.org/W4387333990","https://openalex.org/W3045856890","https://openalex.org/W2509957998","https://openalex.org/W4309247532","https://openalex.org/W4399550897"],"abstract_inverted_index":{"Code":[0],"accompanying":[1],"the":[2,18,36,53,59,87,109],"article":[3],"\"Monotone":[4],"and":[5,51,62,73,82,86,102],"non-monotone":[6],"pace":[7,67],"along":[8],"trajectories":[9],"of":[10,20,58,65],"nonlinear":[11],"differential":[12],"equations,":[13],"with":[14,97],"an":[15],"application":[16],"to":[17],"tempo":[19],"cell":[21],"differentiation\"":[22],"(N.":[23],"Okui).":[24],"The":[25],"archive":[26],"contains:-":[27],"notebooks/pace_GSE279710_v3.ipynb:":[28],"a":[29],"Jupyter":[30],"notebook":[31],"(Google":[32],"Colab)":[33],"that":[34],"downloads":[35],"public":[37],"single-cell":[38],"RNA-seq":[39],"time":[40],"course":[41],"GEO":[42],"GSE279710":[43],"(Shen":[44],"et":[45],"al.,":[46],"Sci":[47],"Data":[48],"12:1238,":[49],"2025)":[50],"reproduces":[52],"analysis":[54],"in":[55],"Section":[56],"8":[57],"article:":[60],"naive":[61],"split-half":[63],"estimates":[64],"sampled":[66],"between":[68],"day":[69],"means,":[70],"bootstrap":[71],"intervals,":[72],"principal-component":[74],"read-outs.-":[75],"figures/fig1_examples.py:":[76],"Figure":[77,84],"1":[78],"(closed-form":[79],"examples).-":[80],"figures/fig2_data.py":[81],"figures/summary_v3.json:":[83],"2":[85],"summary":[88],"statistics":[89],"it":[90],"is":[91],"drawn":[92],"from.":[93],"Requirements:":[94],"Python":[95],"3":[96],"NumPy,":[98],"SciPy,":[99],"pandas,":[100],"scikit-learn":[101],"Matplotlib.":[103],"Random":[104],"seed":[105],"0.":[106],"Released":[107],"under":[108],"MIT":[110],"licence.":[111]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-08T00:00:00"}