{{{#!html Files for the workshop in Bloomington July-August 2017 }}} {{attachment:WP_20170730_13_29_10_small.jpg|class snapshot 1|width="300"}} {{attachment:WP_20170731_13_10_15_Pro.jpg|class snapshot 2|width="320"}} {{attachment:class_photo.jpg|Class group shot|width="800"}} <> = Photos = [[http://www.compucell3d.org/Workshops/Workshop17/SundayJuly30|Sunday, July 30th]] [[http://www.compucell3d.org/Workshops/Workshop17/MondayJuly31|Monday, July 31st]] [[http://www.compucell3d.org/Workshops/Workshop17/TuesdayAugust1|Tuesday, August 1st]] [[http://www.compucell3d.org/Workshops/Workshop17/WednesdayAugust2|Wednesday, August 2nd]] [[http://www.compucell3d.org/Workshops/Workshop17/ThursdayAugust3|Thursday, August 3rd]] [[http://www.compucell3d.org/Workshops/Workshop17/FridayAugust4|Friday, August 4th]] ------- = Maps = {*} [[attachment:Bloomington_and_WoodburnHall.pdf|Bloomington and Woodburn Hall (pdf)|&do=get]] {*} [[attachment:Detailed_IU_map.png|Detailed IU map (png)|&do=get]] {*} [[https://www.google.com/maps/place/Woodburn+Hall,+1100+E+7th+St,+Bloomington,+IN+47405/@39.1684232,-86.5800516,12.29z/data=!4m5!3m4!1s0x886c66c0837a7dd7:0x147532cb28315aaf!8m2!3d39.1681419!4d-86.5200094?hl=en|Google Map]] ------- = Schedules = {*} [[attachment:schedule.docx|Week's Schedule (.docx)|&do=get]] {*} [[attachment:schedule.pdf|Week's Schedule (.pdf)|&do=get]] ------- = Quick reference cards = 1. [[attachment:PythonRefCard_1p.pdf|Single page Python reference card (pdf)|&do=get]] 1. [[attachment:PythonRefCard_8p.pdf|An 8 page, more comprehensive Python reference card (pdf)|&do=get]] 1. [[attachment:CC3D_Quick_Reference_Guide.pdf|CompuCell3D quick reference card (pdf)|&do=get]] ------- = Presentation Slides = == Sunday == ||'''Lecture''' ||'''Python Code(s)''' || ||[[attachment:lec1-intro.pptx||&do=get]] ||[[attachment:lec1.py||&do=get]] || ||[[attachment:lec2-branching-iteration.pptx||&do=get]] ||[[attachment:lec2.py||&do=get]] || ||[[attachment:lec3-strings-approximations.pptx||&do=get]] ||[[attachment:lec3.py||&do=get]] || ||[[attachment:lec4-basic-functions.pptx||&do=get]] || || ||[[attachment:lec5-tuple-lists.pdf||&do=get]] ||[[attachment:lec5_tuples_lists.py||&do=get]] || ||[[attachment:lec6-dictionaries.pptx||&do=get]] ||[[attachment:lec6.py||&do=get]] [[attachment:lec6_recursion_dictionaries.py||&do=get]] || ||[[attachment:lec7-adv-functions.pptx||&do=get]] || || ||[[attachment:lec7-random-walk.pptx||&do=get]] || || . [[attachment:Monday lectures Python ppt and code.zip|Sunday lectures Python ppt and python code.zip|&do=get]] == Monday == ==== AM ==== [[attachment:CC3D-Lecture Morning 1 August 2017v4-1.pptx|Prof. Glazier talk (pptx)|&do=get]] * [[attachment:Priyom Verbal Model from Mark Alber Epithelial paper with annotations.docx|Priyom's Verbal Model from Mark Alber Epithelial paper with annotations (docx)|&do=get]] (Alber [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005533|Article PDF]]). ==== PM ==== [[attachment:Slides_ReactionKinetics-2.pptx|Reaction Kinetics Presentation (ppt)|&do=get]] * [[attachment:Andy RK.zip|Zip file of COPASI, PDFs etc.|&do=get]] == Tuesday == ==== AM ==== [[attachment:PBPK_SBML_modeling.pptx|PBPK modeling in SBML--COPASI (ppt)|&do=get]] * [[attachment:PK_simple_one_compartment.cps||&do=get]] ===== PBPK model of Acetaminophen ===== * [[attachment:BIOMD0000000619.xml|SBML format from BioModels (.xml)|&do=get]] (or get it from directly from [[http://www.ebi.ac.uk/biomodels-main/|BioModels Database]] as model [[http://www.ebi.ac.uk/biomodels-main/BIOMD0000000619|BIOMD0000000619]]) * [[attachment:Acetaminophen_PBPK.cps|COPASI format (.cps)|&do=get]] * [[attachment:Critchley_human_APAP_data.csv|Human ADME data of Critchley et al. (.csv)|&do=get]] ==== PM ==== [[attachment:CC3D Intro.pptx|CC3D Intro (.pptx)|&do=get]] [[attachment:s13628-015-0022-x.pdf|The biophysical nature of cells: potential cell behaviours revealed by analytical and computational studies of cell surface mechanics. R. Magno et al. (pdf)|&do=get]] == Wednesday == [[attachment:MultiScaleModelingWithCC3D-SBML.pptx|MultiScale Modeling With CC3D-SBML (.pptx)|&do=get]] [[attachment:delta-notch.pptx|delta-notch slides (.pptx)|&do=get]] [[attachment:delta-notch.cps|delta-notch in COPASI (.cps)|&do=get]] == Thursday == ==== Priyom Adhyapok's ==== [[attachment:gradient_1.zip|CC3D Gradient 1 (zip)|&do=get]] [[attachment:gradient_2.zip|CC3D Gradient 2 (zip)|&do=get]] [[attachment:gradient_3.zip|CC3D Gradient 3 (zip)|&do=get]] ==== Julio Belmonte's ==== [[attachment:cellcycle_DN.zip|cellcycle_DN (zip)|&do=get]] == Friday == ==== Julio Belmonte's ==== [[attachment:DirectedMovement.zip|Directed Movement files (zip)|&do=get]] [[attachment:CellCompartmentsAndLinks.pptx|Cell Compartments and Links (pptx)|&do=get]] [[attachment:EpithelialSheet.zip|Epithelial Sheet files (zip)|&do=get]] ==== Juliano Gianlupi ==== [[attachment:parameter-scan.pdf|Parameter Scanning (pdf)|&do=get]] ==== Gilberto Thomas ==== [[attachment:HeikosModel (2).zip|Heikos Model (zip)|&do=get]] [[attachment:CancerFlowCgart.pdf|Heiko's Cancer Model 2|&do=get]] <
> (click to download the full size image) ------- {{{#!wiki comment = Attendees' Presentations = * Steven Ruggiero ([[attachment:CC3D-Computational-TB-Ruggiero.pptx|pptx|&do=get]]) ------- }}} = Models, Files, Papers and ''how to ...'' = ==== Doing ODEs in COPASI/SBML as "Global Variables" that are of type "ODE" instead of defining chemical reactions. ==== * [[attachment:Defining ODEs in COPASI--SBML.pptx|Defining ODEs in COPASI/SBML when they really don't look like chemical reactions (pptx)|&do=get]] ==== A chaotic system implemented in COPASI/SBML. ==== * [[attachment:Chaotic Lorenz in COPASI.cps||&do=get]] ==== Holmes et al., Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst ==== * [[attachment:holmes_sup_material.pdf|Holmes_sup_material.pdf|&do=get]] * [[attachment:holmes_et_al.gene_exp_enh_blas.pdf|Holmes et al. Noise Enhances...(pdf)|&do=get]] ==== Hirashima et al., "Cellular Potts modeling of complex multicellular behaviors in tissue morphogenesis" ==== * [[attachment:Hirashima_et_al-2017-Development_Growt.pdf|Hirashima et al-2017-Development, Growth (pdf)|&do=get]]