tag:joss.theoj.org,2005:/papers/edited_by/@majensenJournal of Open Source Software2024-01-29T16:38:15ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/42112024-01-29T16:38:15Z2024-01-30T08:20:19ZChitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulationsaccepted1.02023-02-15 16:12:05 UTC932024-01-29 16:38:15 UTC920245771DavidMalaspinaInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-5420-9534JordiFaraudoInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-6315-499310.21105/joss.05771https://doi.org/10.5281/zenodo.3274725Tcl, Rich Text Formathttps://joss.theoj.org/papers/10.21105/joss.05771.pdfVMD, chitin polymer structure, molecular dynamics, tcltag:joss.theoj.org,2005:Paper/41952023-07-06T15:27:41Z2023-07-07T00:01:21ZMembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranesacceptedv0.1.02023-02-07 20:46:18 UTC872023-07-06 15:27:41 UTC820235380AmiraliHosseinEunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States of America0000-0002-2580-3577AlexanderJ.SodtEunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States of America0000-0002-5570-821210.21105/joss.05380https://doi.org/10.5281/zenodo.8084178Juliahttps://joss.theoj.org/papers/10.21105/joss.05380.pdfbiophysics, molecular dynamics, lipid membranestag:joss.theoj.org,2005:Paper/39702023-02-21T22:04:59Z2023-02-22T00:00:48ZPhaseTypeR: an R package for phase-type distributions in population geneticsacceptedv1.0.42022-10-18 15:40:06 UTC822023-02-21 22:04:59 UTC820235054IkerRivas-GonzálezBioinformatics Research Centre, Aarhus University, Denmark0000-0002-0515-0628LarsNørvangAndersenDepartment of Mathematics, Aarhus University, Denmark0000-0001-6196-8427AsgerHobolthDepartment of Mathematics, Aarhus University, Denmark0000-0003-4056-128610.21105/joss.05054https://doi.org/10.5281/zenodo.7656038Rhttps://joss.theoj.org/papers/10.21105/joss.05054.pdfphase-type distributions, population genetics, ancestral process, coalescent theorytag:joss.theoj.org,2005:Paper/26182023-02-19T10:59:09Z2023-02-20T00:00:30ZComputer-Aided Generation of N-shift RWSacceptedv.1.0.02021-05-03 13:40:47 UTC822023-02-19 10:59:09 UTC820233431BenjaminEdwardBollingEuropean Spallation Source ERIC0000-0002-6650-536510.21105/joss.03431https://doi.org/10.5281/zenodo.7618915Pythonhttps://joss.theoj.org/papers/10.21105/joss.03431.pdfWorkforce scheduling, Shift, Two-shift, Three-shift, Rotating Shift Work, Rotational Workforce, Scheduling, Schedules, Combinatoric-Generator, Cartesian-Producttag:joss.theoj.org,2005:Paper/39142022-12-19T15:08:09Z2022-12-20T00:01:26Zteiphy: A Python Package for Converting TEI XML Collations to NEXUS and Other Formatsacceptedv0.1.22022-09-22 12:35:27 UTC802022-12-19 15:08:09 UTC720224879JoeyMcCollumInstitute for Religion and Critical Inquiry, Australian Catholic University, Australia0000-0002-5647-0365RobertTurnbullMelbourne Data Analytics Platform, University of Melboune, Australia0000-0003-1274-675010.21105/joss.04879https://doi.org/10.5281/zenodo.7455638Pythonhttps://joss.theoj.org/papers/10.21105/joss.04879.pdfphylogenetics, text encoding, TEI, NEXUStag:joss.theoj.org,2005:Paper/36972022-11-07T08:51:46Z2022-11-08T00:00:50Zfars_cleaner: A Python package for downloading and pre-processing vehicle fatality data in the USacceptedv1.2.02022-07-01 16:28:22 UTC792022-11-07 08:51:46 UTC720224678MitchellZ.AbramsDuke University, USA0000-0001-6818-5214CameronR.BassDuke University, USA10.21105/joss.04678https://doi.org/10.5281/zenodo.7249980Pythonhttps://joss.theoj.org/papers/10.21105/joss.04678.pdfFARS, NHTSA, vehicle crash analysis, crashes, road safetytag:joss.theoj.org,2005:Paper/36202022-10-09T08:17:18Z2022-10-10T00:01:33ZPyMSM: Python package for Competing Risks and Multi-State models for Survival Dataacceptedv0.1.72022-05-23 16:51:40 UTC782022-10-09 08:17:18 UTC720224566HagaiRossmanDepartment of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel0000-0002-5613-8004AyyaKeshetDepartment of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel0000-0002-1841-7918MalkaGorfineDepartment of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel0000-0002-1577-662410.21105/joss.04566https://doi.org/10.5281/zenodo.7140849Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04566.pdfmultistate models, survival analysis, competing riskstag:joss.theoj.org,2005:Paper/36132022-09-23T14:45:34Z2022-09-25T16:58:01Zhaldensify: Highly adaptive lasso conditional density estimation in Racceptedv0.2.52022-05-18 15:31:04 UTC772022-09-23 14:45:34 UTC720224522NimaS.HejaziDepartment of Biostatistics, T.H. Chan School of Public Health, Harvard University0000-0002-7127-2789MarkJ.van der LaanDivision of Biostatistics, School of Public Health, University of California, Berkeley, Department of Statistics, University of California, Berkeley0000-0002-1019-8343DavidBenkeserDepartment of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University0000-0002-1019-834310.21105/joss.04522https://doi.org/10.5281/zenodo.7089147Rhttps://joss.theoj.org/papers/10.21105/joss.04522.pdfmachine learning, causal inference, conditional density estimation, generalized propensity score, inverse probability weighting, semiparametric inferencetag:joss.theoj.org,2005:Paper/32532022-07-13T10:07:55Z2022-07-14T00:00:34ZMagphi: Sequence extraction tool from FASTA and GFF3 files using seed pairsacceptedv0.1.62021-12-17 00:01:19 UTC752022-07-13 10:07:55 UTC720224369MagnusG.JespersenDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia0000-0001-9751-9877AndrewHayesDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia0000-0001-8038-1656MarkR.DaviesDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia0000-0001-6141-517910.21105/joss.04369https://doi.org/10.5281/zenodo.6814768Pythonhttps://joss.theoj.org/papers/10.21105/joss.04369.pdfmicrobiology, genomics, genometag:joss.theoj.org,2005:Paper/32482022-03-11T21:29:36Z2022-03-12T00:01:09ZPyBioPAX: biological pathway exchange in Pythonaccepted0.1.02021-12-15 15:55:54 UTC712022-03-11 21:29:36 UTC720224136BenjaminM.GyoriLaboratory of Systems Pharmacology, Harvard Medical School0000-0001-9439-5346CharlesTapleyHoytLaboratory of Systems Pharmacology, Harvard Medical School0000-0003-4423-437010.21105/joss.04136https://doi.org/10.5281/zenodo.6331584Pythonhttps://joss.theoj.org/papers/10.21105/joss.04136.pdfsystems biology, biological pathways, networks