Index

_

__lt__() (orm.measurement_technique.MeasurementTechnique method) (orm.MeasurementTechnique method) (orm.Metabolite method) (orm.metabolite.Metabolite method) (orm.Strain method) (orm.strain.Strain method) __repr__() (orm.orm_base.OrmBase method) __str__() (orm.measurement_technique.MeasurementTechnique method) (orm.MeasurementTechnique method) (orm.orm_base.OrmBase method) __tablename__ (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.Community attribute) (orm.community.Community attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.excel_file.ExcelFile attribute) (orm.ExcelFile attribute) (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.Measurement attribute) (orm.measurement.Measurement attribute) (orm.measurement_context.MeasurementContext attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementContext attribute) (orm.MeasurementTechnique attribute) (orm.Metabolite attribute) (orm.metabolite.Metabolite attribute) (orm.modeling_request.ModelingRequest attribute) (orm.modeling_result.ModelingResult attribute) (orm.ModelingRequest attribute) (orm.ModelingResult attribute) (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) (orm.Project attribute) (orm.project.Project attribute) (orm.project_user.ProjectUser attribute) (orm.ProjectUser attribute) (orm.Strain attribute) (orm.strain.Strain attribute) (orm.Study attribute) (orm.study.Study attribute) (orm.study_metabolite.StudyMetabolite attribute) (orm.study_user.StudyUser attribute) (orm.StudyMetabolite attribute) (orm.StudyUser attribute) (orm.Submission attribute) (orm.submission.Submission attribute) (orm.Taxon attribute) (orm.taxon.Taxon attribute) (orm.User attribute) (orm.user.User attribute) _add_header() (in module data_spreadsheet) _asdict() (orm.orm_base.OrmBase method) _base_bioreplicate_query() (experiment_export_form.ExperimentExportForm method) _build_strain() (in module submission_process) _calculate_x_range() (chart.Chart method) _calculate_y_range() (chart.Chart method) _close_db_connection() (in module global_handlers) _convert_df_units() (chart.Chart method) _convert_units() (chart.Chart method) _create_average_measurement_context() (in module submission_process) _create_average_measurements() (in module submission_process)

_determine_project_type() (submission_form.SubmissionForm method) _extract_args() (comparative_chart_form.ComparativeChartForm method) _extract_bioreplicate_args() (experiment_export_form.ExperimentExportForm method) _extract_csv_args() (experiment_export_form.ExperimentExportForm method) _extract_r_summary() (in module modeling_tasks) _fetch_experiment() (in module experiments) _fetch_study() (in module studies) _fetch_user() (in module global_handlers) _fill_sheet() (in module data_spreadsheet) _find_custom_strain() (in module submission_process) _find_project_id() (submission_form.SubmissionForm method) _find_study_id() (submission_form.SubmissionForm method) _format_row_list_error() (in module submission_process) _get_expected_column_names() (in module submission_process) _get_orcid_root_url() (in module orcid) _get_scatter_params() (chart.Chart method) _html_cache (help.HelpPages attribute) _init_compare_data() (in module comparison) _init_submission_form() (in module upload) _init_upload_form() (in module upload) _iterate_error_messages() (in module base_form) _make_session_permanent() (in module global_handlers) _one_or_error() (in module util) _open_db_connection() (in module global_handlers) _predict() (orm.modeling_result.ModelingResult method) (orm.ModelingResult method) _predict_baranyi_roberts() (orm.modeling_result.ModelingResult method) (orm.ModelingResult method) _predict_easy_linear() (orm.modeling_result.ModelingResult method) (orm.ModelingResult method) _predict_logistic() (orm.modeling_result.ModelingResult method) (orm.ModelingResult method) _process_modeling_request() (in module modeling_tasks) _read_raw_json() (r_script.RScript method) _redirect_to_login() (in module global_handlers) _render_forbidden() (in module global_handlers) _render_not_found() (in module global_handlers) _render_server_error() (in module global_handlers) _request_is_ajax() (in module help) (in module upload) _save_communities() (in module submission_process) _save_compartments() (in module submission_process) _save_experiments() (in module submission_process) _save_measurement_techniques() (in module submission_process) _save_measurements() (in module submission_process) _save_project() (in module submission_process) _save_study() (in module submission_process) _step2_partial() (in module upload) _step3_partial() (in module upload) _step4_partial() (in module upload) _step5_partial() (in module upload) _text_cache (help.HelpPages attribute) _user_login_show() (in module users) _user_login_submit() (in module users) _validate_inclusion() (orm.orm_base.OrmBase method) _validate_state() (orm.modeling_request.ModelingRequest method) (orm.modeling_result.ModelingResult method) (orm.ModelingRequest method) (orm.ModelingResult method) _validate_type() (orm.modeling_request.ModelingRequest method) (orm.modeling_result.ModelingResult method) (orm.ModelingRequest method) (orm.ModelingResult method) _validate_unique_project_names() (submission_form.SubmissionForm method) _validate_uniqueness() (base_form.BaseForm method) _value() (admin.AppJSONField method)

A

add_df() (chart.Chart method) add_model_df() (chart.Chart method) addedCompartmentId (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) addedCompartmentName (upload_step5_form.UploadStep5Form.ExperimentForm.PerturbationForm attribute) admin module APP_ENV (in module routes) AppAdminIndexView (class in admin)

AppDateTimeField (class in admin) AppJSONField (class in admin) apply_log_transform() (in module log_transform) AppModelConverter (class in admin) AppView (class in admin) assets module authenticate_user() (in module orcid) averageMass (orm.Metabolite attribute) (orm.metabolite.Metabolite attribute)

B

base_form module BaseForm (class in base_form) Bioreplicate (class in orm) (class in orm.bioreplicate) bioreplicate (orm.Measurement attribute) (orm.measurement.Measurement attribute) (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) bioreplicate_uuids (experiment_export_form.ExperimentExportForm attribute) bioreplicateId (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute)

bioreplicates (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.Study attribute) (orm.study.Study attribute) (upload_step5_form.UploadStep5Form.ExperimentForm attribute) biosampleUrl (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.BioreplicateForm attribute) bootstrap_study() (in module dev) build_chart() (comparative_chart_form.ComparativeChartForm method) build_techniques() (orm.Submission method) (orm.submission.Submission method)

C

calculatedAt (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) calculationType (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) can_export (admin.AppView attribute) can_view_details (admin.AppView attribute) celery module cell_count_units (chart.Chart attribute) (comparative_chart_form.ComparativeChartForm attribute) CELL_COUNT_UNITS (in module chart) cfu_count_units (chart.Chart attribute) (comparative_chart_form.ComparativeChartForm attribute) CFU_COUNT_UNITS (in module chart) chart module Chart (class in chart) chebi_id (orm.study_metabolite.StudyMetabolite attribute) (orm.StudyMetabolite attribute) chebi_url() (in module filters.urls) chebiId (orm.Metabolite attribute) (orm.metabolite.Metabolite attribute) clamp_x_data (chart.Chart attribute) clauses (search_form.SearchForm attribute) CO2 (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) coefficients (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) column_type_formatters (admin.AppView attribute) column_type_formatters_detail (admin.AppView attribute) column_type_formatters_export (admin.AppView attribute) communities (orm.Study attribute) (orm.study.Study attribute) (upload_step4_form.UploadStep4Form attribute) Community (class in orm) (class in orm.community) community (orm.Experiment attribute) (orm.experiment.Experiment attribute) communityId (orm.Experiment attribute) (orm.experiment.Experiment attribute) communityName (upload_step5_form.UploadStep5Form.ExperimentForm attribute) comparative_chart_form module ComparativeChartForm (class in comparative_chart_form) comparison module comparison_chart_fragment() (in module comparison) comparison_clear_action() (in module comparison) comparison_show_page() (in module comparison) comparison_update_json() (in module comparison) Compartment (class in orm) (class in orm.compartment) compartment (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.Measurement attribute) (orm.measurement.Measurement attribute) (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute)

compartmentId (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) compartmentNames (upload_step5_form.UploadStep5Form.ExperimentForm attribute) compartments (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.Study attribute) (orm.study.Study attribute) (upload_step4_form.UploadStep4Form attribute) completed_step_count (orm.Submission property) (orm.submission.Submission property) config module content (orm.excel_file.ExcelFile attribute) (orm.ExcelFile attribute) context (orm.Measurement attribute) (orm.measurement.Measurement attribute) context_relationship (orm.Measurement attribute) (orm.measurement.Measurement attribute) contextId (orm.Measurement attribute) (orm.measurement.Measurement attribute) conversion module convert_datetime() (admin.AppModelConverter method) convert_JSON() (admin.AppModelConverter method) convert_measurement_units() (in module conversion) convert_time() (in module conversion) create_excel() (in module data_spreadsheet) createdAt (orm.excel_file.ExcelFile attribute) (orm.ExcelFile attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (orm.modeling_request.ModelingRequest attribute) (orm.modeling_result.ModelingResult attribute) (orm.ModelingRequest attribute) (orm.ModelingResult attribute) (orm.Study attribute) (orm.study.Study attribute) (orm.Submission attribute) (orm.submission.Submission attribute) (orm.User attribute) (orm.user.User attribute) createzip() (in module util) csrf (search_form.SearchFormClause.Meta attribute) (upload_step2_form.UploadStep2Form.NewStrainForm.Meta attribute) (upload_step3_form.UploadStep3Form.TechniqueForm.Meta attribute) (upload_step4_form.UploadStep4Form.CommunityForm.Meta attribute) (upload_step4_form.UploadStep4Form.CompartmentForm.Meta attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.BioreplicateForm.Meta attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.Meta attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.PerturbationForm.Meta attribute) csv_column_name() (orm.measurement_technique.MeasurementTechnique method) (orm.MeasurementTechnique method) csv_separator (experiment_export_form.ExperimentExportForm attribute) cultivationMode (orm.Experiment attribute) (orm.experiment.Experiment attribute) (upload_step5_form.UploadStep5Form.ExperimentForm attribute) custom_strains (upload_step2_form.UploadStep2Form attribute)

D

data_left (chart.Chart attribute) data_right (chart.Chart attribute) data_spreadsheet module dataFile (orm.Submission attribute) (orm.submission.Submission attribute) dataFileId (orm.Submission attribute) (orm.submission.Submission attribute) db module db_session (comparative_chart_form.ComparativeChartForm attribute) (experiment_export_form.ExperimentExportForm attribute) (submission_form.SubmissionForm attribute) DEFAULT_STUDY_DESIGN (in module submission_form) defined (orm.Strain attribute) (orm.strain.Strain attribute) delete_submission_action() (in module submissions) description (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) (orm.Strain attribute) (orm.strain.Strain attribute) (upload_step2_form.UploadStep2Form.NewStrainForm attribute) (upload_step3_form.UploadStep3Form.TechniqueForm attribute) (upload_step5_form.UploadStep5Form.ExperimentForm attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.PerturbationForm attribute)

description() (orm.Study method) (orm.study.Study method) dev module download_data_template_xlsx() (in module upload) download_excel_file() (in module excel_files) dump_routes() (in module routes)

E

edit_submission_action() (in module submissions) embargoExpiresAt (orm.Study attribute) (orm.study.Study attribute) empty_coefficients() (orm.modeling_result.ModelingResult class method) (orm.ModelingResult class method) empty_fit() (orm.modeling_result.ModelingResult class method) (orm.ModelingResult class method) empty_inputs() (orm.modeling_result.ModelingResult class method) (orm.ModelingResult class method) error (orm.modeling_request.ModelingRequest attribute) (orm.modeling_result.ModelingResult attribute) (orm.ModelingRequest attribute) (orm.ModelingResult attribute) error_messages (base_form.BaseForm property) error_messages() (submission_form.SubmissionForm method) errors module errors (submission_form.SubmissionForm attribute) excel module excel_files module ExcelFile (class in orm) (class in orm.excel_file) execute_into_df() (in module db) execute_text() (in module db) Experiment (class in orm) (class in orm.experiment) experiment (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute)

experiment_export_form module experiment_show_page() (in module experiments) ExperimentCompartment (class in orm) (class in orm.experiment_compartment) experimentCompartments (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.Study attribute) (orm.study.Study attribute) ExperimentExportForm (class in experiment_export_form) experimentId (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) experiments module experiments (experiment_export_form.ExperimentExportForm attribute) (orm.Community attribute) (orm.community.Community attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.Study attribute) (orm.study.Study attribute) (upload_step5_form.UploadStep5Form attribute) export_model_csv() (in module model_export) export_to_xlsx() (in module excel) external_link() (in module filters.urls) extract_sheets() (orm.excel_file.ExcelFile method) (orm.ExcelFile method)

F

fetch_all_metabolites() (submission_form.SubmissionForm method) fetch_metabolites_for_technique() (submission_form.SubmissionForm method) fetch_taxa() (submission_form.SubmissionForm method) filename (orm.excel_file.ExcelFile attribute) (orm.ExcelFile attribute) filter_keys() (orm.orm_base.OrmBase class method) filters module filters.lists module filters.numbers module filters.time module

filters.urls module find_for_study() (orm.Bioreplicate static method) (orm.bioreplicate.Bioreplicate static method) (orm.Strain static method) (orm.strain.Strain static method) find_last_submission() (orm.Study method) (orm.study.Study method) fit (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) flask_db module FORMATTERS (in module admin) from_upload() (orm.excel_file.ExcelFile class method) (orm.ExcelFile class method)

G

generate_chart_df() (orm.modeling_result.ModelingResult method) (orm.ModelingResult method) generate_public_id() (orm.Experiment static method) (orm.experiment.Experiment static method) (orm.Project static method) (orm.project.Project static method) (orm.Study static method) (orm.study.Study static method) get_bioreplicates() (orm.measurement_technique.MeasurementTechnique method) (orm.MeasurementTechnique method) get_chart_label() (orm.measurement_context.MeasurementContext method) (orm.MeasurementContext method) get_df() (comparative_chart_form.ComparativeChartForm method) (orm.measurement_context.MeasurementContext method) (orm.MeasurementContext method)

get_experiment_data() (experiment_export_form.ExperimentExportForm method) get_grouped_contexts() (orm.measurement_technique.MeasurementTechnique method) (orm.MeasurementTechnique method) get_login_url() (in module orcid) get_strains() (orm.Community method) (orm.community.Community method) get_subject() (orm.measurement_context.MeasurementContext method) (orm.MeasurementContext method) get_subjects_for_bioreplicate() (orm.measurement_technique.MeasurementTechnique method) (orm.MeasurementTechnique method) get_template() (base_form.BaseForm method) get_user_url() (in module orcid) global_handlers module group_by_unique_name() (in module util)

H

H2 (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) has_error() (submission_form.SubmissionForm method) has_valid_project_data() (submission_form.SubmissionForm method) has_valid_study_data() (submission_form.SubmissionForm method) help module

help_index_page() (in module help) help_link() (in module filters.urls) HELP_PAGES (in module help) help_show_page() (in module help) HelpPages (class in help) html_step_classes() (submission_form.SubmissionForm method) humanize_camelcased_string() (in module util) humanized_size (orm.excel_file.ExcelFile property) (orm.ExcelFile property)

I

id (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.Community attribute) (orm.community.Community attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.excel_file.ExcelFile attribute) (orm.ExcelFile attribute) (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.Measurement attribute) (orm.measurement.Measurement attribute) (orm.measurement_context.MeasurementContext attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementContext attribute) (orm.MeasurementTechnique attribute) (orm.Metabolite attribute) (orm.metabolite.Metabolite attribute) (orm.modeling_request.ModelingRequest attribute) (orm.modeling_result.ModelingResult attribute) (orm.ModelingRequest attribute) (orm.ModelingResult attribute) (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) (orm.project_user.ProjectUser attribute) (orm.ProjectUser attribute) (orm.Strain attribute) (orm.strain.Strain attribute) (orm.study_metabolite.StudyMetabolite attribute) (orm.study_user.StudyUser attribute) (orm.StudyMetabolite attribute) (orm.StudyUser attribute) (orm.Submission attribute) (orm.submission.Submission attribute) (orm.Taxon attribute) (orm.taxon.Taxon attribute) (orm.User attribute) (orm.user.User attribute) inaccessible_callback() (admin.AppView method) includeStd (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (upload_step3_form.UploadStep3Form.TechniqueForm attribute)

index() (admin.AppAdminIndexView method) init_admin() (in module admin) init_assets() (in module assets) init_celery() (in module celery) init_config() (in module config) init_flask_db() (in module flask_db) init_global_handlers() (in module global_handlers) init_plotly() (in module plotly) init_routes() (in module routes) init_template_filters() (in module template_filters) init_timing() (in module timing) initialPh (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) initialTemperature (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) inoculumConcentration (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) inoculumVolume (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) inputs (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) insert_from_csv_string() (orm.Measurement class method) (orm.measurement.Measurement class method) is_accessible() (admin.AppView method) is_growth (orm.measurement_technique.MeasurementTechnique property) (orm.MeasurementTechnique property) is_non_negative_float() (in module util) isAdmin (orm.User attribute) (orm.user.User attribute) isBlank (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.BioreplicateForm attribute) isControl (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.BioreplicateForm attribute) isPublishable() (orm.Study method) (orm.study.Study method) isPublished() (orm.Study method) (orm.study.Study method)

J

jobUuid (orm.modeling_request.ModelingRequest attribute) (orm.ModelingRequest attribute)

join_tag() (in module filters.lists) json_formatter() (in module admin)

L

lastLoginAt (orm.User attribute) (orm.user.User attribute) left_axis_ids (comparative_chart_form.ComparativeChartForm attribute) legend_position (chart.Chart attribute) log_db_timing() (in module timing) log_left (chart.Chart attribute) log_request_timing() (in module timing) log_right (chart.Chart attribute) log_transform module

LOGGER (in module modeling_tasks) (in module r_script) logic_operator (search_form.SearchFormClause attribute) LoginRequired long_name (orm.measurement_technique.MeasurementTechnique property) (orm.MeasurementTechnique property) (orm.modeling_request.ModelingRequest property) (orm.ModelingRequest property) long_name_with_subject_type (orm.measurement_technique.MeasurementTechnique property) (orm.MeasurementTechnique property)

M

manageable_by_user() (orm.Study method) (orm.study.Study method) managedProjects (orm.User attribute) (orm.user.User attribute) managedStudies (orm.User attribute) (orm.user.User attribute) managerUuids (orm.Project property) (orm.project.Project property) (orm.Study property) (orm.study.Study property) map_scientific() (in module filters.numbers) markdown (help.HelpPages attribute) Measurement (class in orm) (class in orm.measurement) measurement_context_ids (comparative_chart_form.ComparativeChartForm attribute) measurement_contexts (comparative_chart_form.ComparativeChartForm attribute) MEASUREMENT_RATIOS (in module conversion) MeasurementContext (class in orm) (class in orm.measurement_context) measurementContext (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) measurementContextId (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) measurementContexts (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (orm.Study attribute) (orm.study.Study attribute) measurements (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.measurement_context.MeasurementContext attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementContext attribute) (orm.MeasurementTechnique attribute) (orm.Study attribute) (orm.study.Study attribute) MeasurementTechnique (class in orm) (class in orm.measurement_technique) measurementTechniques (orm.Study attribute) (orm.study.Study attribute) mediumName (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) mediumUrl (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) Metabolite (class in orm) (class in orm.metabolite) metabolite (orm.study_metabolite.StudyMetabolite attribute) (orm.StudyMetabolite attribute) metabolite_units (chart.Chart attribute) (comparative_chart_form.ComparativeChartForm attribute) METABOLITE_UNITS (in module chart) metaboliteIds (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (upload_step3_form.UploadStep3Form.TechniqueForm attribute) metabolites module metabolites (orm.Study attribute) (orm.study.Study attribute) metabolites_completion_json() (in module metabolites) migrate module mixed_units_left (chart.Chart attribute) mixed_units_right (chart.Chart attribute) model_df_indices (chart.Chart attribute) model_export module model_form_converter (admin.AppView attribute) model_name (orm.modeling_result.ModelingResult property) (orm.ModelingResult property) MODEL_NAMES (in module orm.modeling_request) (in module orm.modeling_result) modeling_tasks module ModelingRequest (class in orm) (class in orm.modeling_request)

modelingRequests (orm.Study attribute) (orm.study.Study attribute) ModelingResult (class in orm) (class in orm.modeling_result) modelingResults (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) (orm.Study attribute) (orm.study.Study attribute) module admin assets base_form celery chart comparative_chart_form comparison config conversion data_spreadsheet db dev errors excel excel_files experiment_export_form experiments filters filters.lists filters.numbers filters.time filters.urls flask_db global_handlers help log_transform metabolites migrate model_export modeling_tasks orcid orm orm.bioreplicate orm.community orm.compartment orm.excel_file orm.experiment orm.experiment_compartment orm.measurement orm.measurement_context orm.measurement_technique orm.metabolite orm.modeling_request orm.modeling_result orm.orm_base orm.perturbation orm.project orm.project_user orm.strain orm.study orm.study_metabolite orm.study_user orm.submission orm.taxon orm.user plotly projects r_script routes search search_form static strains studies submission_form submission_process submissions template_filters timing upload upload_step2_form upload_step3_form upload_step4_form upload_step5_form users util

N

N2 (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) name (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.Community attribute) (orm.community.Community attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.Metabolite attribute) (orm.metabolite.Metabolite attribute) (orm.Strain attribute) (orm.strain.Strain attribute) (orm.Taxon attribute) (orm.taxon.Taxon attribute) (orm.User attribute) (orm.user.User attribute) (upload_step2_form.UploadStep2Form.NewStrainForm attribute) (upload_step4_form.UploadStep4Form.CommunityForm attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) (upload_step5_form.UploadStep5Form.ExperimentForm attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.BioreplicateForm attribute)

name() (orm.Project method) (orm.project.Project method) (orm.Study method) (orm.study.Study method) ncbi_url() (in module filters.urls) NCBId (orm.Strain attribute) (orm.strain.Strain attribute) ncbiId (orm.Taxon attribute) (orm.taxon.Taxon attribute) new_submission_action() (in module submissions) newCommunityId (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) newCommunityName (upload_step5_form.UploadStep5Form.ExperimentForm.PerturbationForm attribute)

O

O2 (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) oldCommunityId (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) oldCommunityName (upload_step5_form.UploadStep5Form.ExperimentForm.PerturbationForm attribute) option (search_form.SearchFormClause attribute) orcid module orcidId (orm.User attribute) (orm.user.User attribute) orcidToken (orm.User attribute) (orm.user.User attribute) orcidUrl (orm.User property) (orm.user.User property) orm module orm.bioreplicate module orm.community module orm.compartment module orm.excel_file module orm.experiment module orm.experiment_compartment module orm.measurement module orm.measurement_context module orm.measurement_technique module orm.metabolite module orm.modeling_request module orm.modeling_result module

orm.orm_base module orm.perturbation module orm.project module orm.project_user module orm.strain module orm.study module orm.study_metabolite module orm.study_user module orm.submission module orm.taxon module orm.user module OrmBase (class in orm.orm_base) ownedProjects (orm.User attribute) (orm.user.User attribute) ownedStudies (orm.User attribute) (orm.user.User attribute) owner (orm.Project attribute) (orm.project.Project attribute) (orm.Study attribute) (orm.study.Study attribute) owner_relationship (orm.Study attribute) (orm.study.Study attribute) (orm.User attribute) (orm.user.User attribute) ownerUniqueID (orm.Project attribute) (orm.project.Project attribute) (orm.Study attribute) (orm.study.Study attribute)

P

permalink_query (comparative_chart_form.ComparativeChartForm property) persist_submission_to_database() (in module submission_process) Perturbation (class in orm) (class in orm.perturbation) perturbations (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.Study attribute) (orm.study.Study attribute) (upload_step5_form.UploadStep5Form.ExperimentForm attribute) plotly module PLOTLY_TEMPLATE (in module chart) position (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.BioreplicateForm attribute) pressure (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) prettify_name() (admin.AppView method) process_formdata() (admin.AppDateTimeField method) (admin.AppJSONField method) process_modeling_request() (in module modeling_tasks) process_once() (help.HelpPages method) Project (class in orm) (class in orm.project) project (orm.project_user.ProjectUser attribute) (orm.ProjectUser attribute) (orm.Study attribute) (orm.study.Study attribute) (orm.Submission attribute) (orm.submission.Submission attribute) project_id (submission_form.SubmissionForm attribute) project_show_page() (in module projects) projectDescription (orm.Project attribute) (orm.project.Project attribute)

projectId (orm.Project attribute) (orm.project.Project attribute) projectName (orm.Project attribute) (orm.project.Project attribute) projects module projectUniqueID (orm.Project attribute) (orm.project.Project attribute) (orm.project_user.ProjectUser attribute) (orm.ProjectUser attribute) (orm.Study attribute) (orm.study.Study attribute) (orm.Submission attribute) (orm.submission.Submission attribute) ProjectUser (class in orm) (class in orm.project_user) projectUsers (orm.Project attribute) (orm.project.Project attribute) (orm.User attribute) (orm.user.User attribute) properties_description (orm.Compartment property) (orm.compartment.Compartment property) publicId (orm.Experiment attribute) (orm.experiment.Experiment attribute) publicId() (orm.Project method) (orm.project.Project method) (orm.Study method) (orm.study.Study method) publish() (orm.Study method) (orm.study.Study method) publishableAt (orm.Study attribute) (orm.study.Study attribute) publishedAt (orm.Study attribute) (orm.study.Study attribute)

R

r_script module read_flat_json() (r_script.RScript method) read_key_value_json() (r_script.RScript method) record_formatter() (in module admin) RED (in module data_spreadsheet) relative_time() (in module filters.time) removedCompartmentId (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) removedCompartmentName (upload_step5_form.UploadStep5Form.ExperimentForm.PerturbationForm attribute) render_html() (help.HelpPages method) request (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) requestId (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute)

results (orm.modeling_request.ModelingRequest attribute) (orm.ModelingRequest attribute) right_axis_ids (comparative_chart_form.ComparativeChartForm attribute) root_dir (help.HelpPages attribute) root_path (r_script.RScript attribute) routes module RScript (class in r_script) rscript_exe (r_script.RScript attribute) rSummary (orm.modeling_result.ModelingResult attribute) (orm.ModelingResult attribute) run() (in module migrate) (r_script.RScript method)

S

save() (submission_form.SubmissionForm method) search module search() (help.HelpPages method) search_by_name() (orm.Metabolite static method) (orm.metabolite.Metabolite static method) (orm.Taxon static method) (orm.taxon.Taxon static method) search_form module search_index_page() (in module search) SearchForm (class in search_form) SearchFormClause (class in search_form) SearchFormClause.Meta (class in search_form) short_name (orm.measurement_technique.MeasurementTechnique property) (orm.MeasurementTechnique property) (orm.Taxon property) (orm.taxon.Taxon property) size (orm.excel_file.ExcelFile attribute) (orm.ExcelFile attribute) species (upload_step2_form.UploadStep2Form.NewStrainForm attribute) start_db_timing() (in module timing) start_request_timing() (in module timing) startTimepoint (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) (upload_step5_form.UploadStep5Form.ExperimentForm.PerturbationForm attribute) state (orm.modeling_request.ModelingRequest attribute) (orm.modeling_result.ModelingResult attribute) (orm.ModelingRequest attribute) (orm.ModelingResult attribute) static module static_about_page() (in module static) static_home_page() (in module static) std (orm.Measurement attribute) (orm.measurement.Measurement attribute) step (submission_form.SubmissionForm attribute) stirringMode (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) stirringSpeed (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute) Strain (class in orm) (class in orm.strain) strainIdentifiers (upload_step4_form.UploadStep4Form.CommunityForm attribute) strainIds (orm.Community attribute) (orm.community.Community attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) strains module strains (orm.Study attribute) (orm.study.Study attribute) (upload_step2_form.UploadStep2Form attribute) studies module studies (orm.Project attribute) (orm.project.Project attribute) Study (class in orm) (class in orm.study) study (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.Community attribute) (orm.community.Community attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.Measurement attribute) (orm.measurement.Measurement attribute) (orm.measurement_context.MeasurementContext attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementContext attribute) (orm.MeasurementTechnique attribute) (orm.modeling_request.ModelingRequest attribute) (orm.ModelingRequest attribute) (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) (orm.Strain attribute) (orm.strain.Strain attribute) (orm.study_metabolite.StudyMetabolite attribute) (orm.study_user.StudyUser attribute) (orm.StudyMetabolite attribute) (orm.StudyUser attribute) (orm.Submission attribute) (orm.submission.Submission attribute) study_chart_fragment() (in module studies)

study_download_data_zip() (in module studies) study_download_models_csv() (in module studies) study_export_page() (in module studies) study_export_preview_fragment() (in module studies) study_id (submission_form.SubmissionForm attribute) study_manage_page() (in module studies) study_modeling_chart_fragment() (in module studies) study_modeling_check_json() (in module studies) study_modeling_submit_action() (in module studies) study_show_page() (in module studies) study_visualize_page() (in module studies) studyDescription (orm.Study attribute) (orm.study.Study attribute) studyDesign (orm.Submission attribute) (orm.submission.Submission attribute) studyId (orm.Bioreplicate attribute) (orm.bioreplicate.Bioreplicate attribute) (orm.Community attribute) (orm.community.Community attribute) (orm.Compartment attribute) (orm.compartment.Compartment attribute) (orm.Experiment attribute) (orm.experiment.Experiment attribute) (orm.experiment_compartment.ExperimentCompartment attribute) (orm.ExperimentCompartment attribute) (orm.Measurement attribute) (orm.measurement.Measurement attribute) (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) (orm.modeling_request.ModelingRequest attribute) (orm.ModelingRequest attribute) (orm.Perturbation attribute) (orm.perturbation.Perturbation attribute) (orm.Strain attribute) (orm.strain.Strain attribute) (orm.Study attribute) (orm.study.Study attribute) (orm.study_metabolite.StudyMetabolite attribute) (orm.StudyMetabolite attribute) StudyMetabolite (class in orm) (class in orm.study_metabolite) studyMetabolites (orm.Metabolite attribute) (orm.metabolite.Metabolite attribute) (orm.Study attribute) (orm.study.Study attribute) studyName (orm.Study attribute) (orm.study.Study attribute) studyUniqueID (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (orm.Study attribute) (orm.study.Study attribute) (orm.study_user.StudyUser attribute) (orm.StudyUser attribute) (orm.Submission attribute) (orm.submission.Submission attribute) studyURL (orm.Study attribute) (orm.study.Study attribute) StudyUser (class in orm) (class in orm.study_user) studyUsers (orm.Study attribute) (orm.study.Study attribute) (orm.User attribute) (orm.user.User attribute) studyUuids (orm.Project property) (orm.project.Project property) subject_short_name (orm.measurement_technique.MeasurementTechnique property) (orm.MeasurementTechnique property) subjectId (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) subjectId() (orm.Measurement method) (orm.measurement.Measurement method) subjectType (orm.measurement_context.MeasurementContext attribute) (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementContext attribute) (orm.MeasurementTechnique attribute) (upload_step3_form.UploadStep3Form.TechniqueForm attribute) subjectType() (orm.Measurement method) (orm.measurement.Measurement method) Submission (class in orm) (class in orm.submission) submission (submission_form.SubmissionForm attribute) submission_form module submission_process module SubmissionForm (class in submission_form) submissions module submissions (orm.User attribute) (orm.user.User attribute)

T

taxa_completion_json() (in module strains) Taxon (class in orm) (class in orm.taxon) technique (orm.Measurement attribute) (orm.measurement.Measurement attribute) (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) TECHNIQUE_DESCRIPTIONS (in module data_spreadsheet) technique_descriptions() (submission_form.SubmissionForm method) TECHNIQUE_LONG_NAMES (in module orm.measurement_technique) TECHNIQUE_SHORT_NAMES (in module orm.measurement_technique) techniqueId (orm.measurement_context.MeasurementContext attribute) (orm.MeasurementContext attribute) techniques (upload_step3_form.UploadStep3Form attribute) template_filters module templates_dir (help.HelpPages attribute) time_units (chart.Chart attribute) (comparative_chart_form.ComparativeChartForm attribute) TIME_UNITS (in module data_spreadsheet)

timeInHours() (orm.Measurement method) (orm.measurement.Measurement method) timeInSeconds (orm.Measurement attribute) (orm.measurement.Measurement attribute) timepointCount (upload_step5_form.UploadStep5Form.ExperimentForm attribute) timeUnits (orm.Study attribute) (orm.study.Study attribute) (upload_step5_form.UploadStep5Form attribute) timing module title (chart.Chart attribute) to_html() (chart.Chart method) trim_lines() (in module util) type (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (orm.modeling_request.ModelingRequest attribute) (orm.modeling_result.ModelingResult attribute) (orm.ModelingRequest attribute) (orm.ModelingResult attribute) (submission_form.SubmissionForm attribute) (upload_step3_form.UploadStep3Form.TechniqueForm attribute)

U

units (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (upload_step3_form.UploadStep3Form.TechniqueForm attribute) update() (orm.orm_base.OrmBase method) update_project() (submission_form.SubmissionForm method) update_strains() (submission_form.SubmissionForm method) update_study_design() (submission_form.SubmissionForm method) updatedAt (orm.measurement_technique.MeasurementTechnique attribute) (orm.MeasurementTechnique attribute) (orm.modeling_request.ModelingRequest attribute) (orm.modeling_result.ModelingResult attribute) (orm.ModelingRequest attribute) (orm.ModelingResult attribute) (orm.Study attribute) (orm.study.Study attribute) (orm.Submission attribute) (orm.submission.Submission attribute) (orm.User attribute) (orm.user.User attribute) upload module upload_spreadsheet_preview_fragment() (in module upload) upload_status_page() (in module upload) upload_step1_page() (in module upload) upload_step2_form module upload_step2_page() (in module upload) upload_step3_form module upload_step3_page() (in module upload) upload_step4_form module upload_step4_page() (in module upload) upload_step5_form module upload_step5_page() (in module upload) upload_step6_page() (in module upload) upload_step7_page() (in module upload) UploadStep2Form (class in upload_step2_form) UploadStep2Form.NewStrainForm (class in upload_step2_form) UploadStep2Form.NewStrainForm.Meta (class in upload_step2_form) UploadStep3Form (class in upload_step3_form) UploadStep3Form.TechniqueForm (class in upload_step3_form) UploadStep3Form.TechniqueForm.Meta (class in upload_step3_form)

UploadStep4Form (class in upload_step4_form) UploadStep4Form.CommunityForm (class in upload_step4_form) UploadStep4Form.CommunityForm.Meta (class in upload_step4_form) UploadStep4Form.CompartmentForm (class in upload_step4_form) UploadStep4Form.CompartmentForm.Meta (class in upload_step4_form) UploadStep5Form (class in upload_step5_form) UploadStep5Form.ExperimentForm (class in upload_step5_form) UploadStep5Form.ExperimentForm.BioreplicateForm (class in upload_step5_form) UploadStep5Form.ExperimentForm.BioreplicateForm.Meta (class in upload_step5_form) UploadStep5Form.ExperimentForm.Meta (class in upload_step5_form) UploadStep5Form.ExperimentForm.PerturbationForm (class in upload_step5_form) UploadStep5Form.ExperimentForm.PerturbationForm.Meta (class in upload_step5_form) User (class in orm) (class in orm.user) user (orm.project_user.ProjectUser attribute) (orm.ProjectUser attribute) (orm.study_user.StudyUser attribute) (orm.StudyUser attribute) (orm.Submission attribute) (orm.submission.Submission attribute) user_backdoor_page() (in module users) user_claim_project_action() (in module users) user_claim_study_action() (in module users) user_login_page() (in module users) user_logout_action() (in module users) user_show_page() (in module users) users module userUniqueID (orm.project_user.ProjectUser attribute) (orm.ProjectUser attribute) (orm.Strain attribute) (orm.strain.Strain attribute) (orm.study_user.StudyUser attribute) (orm.StudyUser attribute) (orm.Submission attribute) (orm.submission.Submission attribute) util module uuid (orm.User attribute) (orm.user.User attribute) uuid() (orm.Project method) (orm.project.Project method) (orm.Study method) (orm.study.Study method)

V

VALID_STATES (in module orm.modeling_request) (in module orm.modeling_result) VALID_TYPES (in module orm.modeling_request) (in module orm.modeling_result) validate_bioreplicates() (upload_step5_form.UploadStep5Form.ExperimentForm method) validate_communities() (upload_step4_form.UploadStep4Form method) validate_compartments() (upload_step4_form.UploadStep4Form method) validate_custom_strains() (upload_step2_form.UploadStep2Form method) validate_data_file() (in module submission_process)

validate_experiments() (upload_step5_form.UploadStep5Form method) value (orm.Measurement attribute) (orm.measurement.Measurement attribute) (search_form.SearchFormClause attribute) visible_to_user() (orm.Study method) (orm.study.Study method) volume (orm.Compartment attribute) (orm.compartment.Compartment attribute) (upload_step4_form.UploadStep4Form.CompartmentForm attribute)

W

WHITE (in module data_spreadsheet) width (chart.Chart attribute)

write_csv() (r_script.RScript method) write_json() (r_script.RScript method)