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Study Organization and Documentation

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Synapse helps organize and manage collections of research outputs. Learn how information is organized in Synapse.

Study Naming

MODEL-AD data and metadata are organized by site and study.

Study type

How many strains?

Naming convention

Example names

Primary screen

Many

Site_PrimaryScreen

  • Jax.IU.Pitt_PrimaryScreen

  • UCI_PrimaryScreen

Strain validation

Many

Site_StrainValidation

  • Jax.IU.Pitt_StrainValidation

  • UCI_StrainValidation

Deep phenotyping

Many

Site_Model

  • Jax.IU.Pitt_APOE4_Trem2

  • UCI_5XFAD

Pharmacokinetic (PK)

One

Site_Model_Drug

  • Jax.IU.Pitt_5XFAD_Verubecestat

Pilot Studies

  • Microbiome

  • Proteomics and Metabolomics

Many

Site_StudyType_Pilot

  • Jax.IU.Pitt_MicrobiomePilot Link

  • Jax.IU.Pitt.Proteomics_Metabolomics_Pilot Link

Study Description

Each study should be accompanied by a brief study description that includes the species, genetic background, a link to the Jax Datasheet (if available) or a description of how the animals were created.

Download the in-progress study description template.

Assay Description

Each assessment should be accompanied by a brief description with information about the assessment procedures, data generation and processing, and analytical methods. This information is often described in the Materials and Methods section of a manuscript. This is a good opportunity to provide details that may not be included in the final manuscript.

TODO A methods description template will be made available here.

Issues to clarify include:

  • File naming conventions

  • Assay-specific examples. Need a list of most common assays.

    • RNA sequencing

    • Behavioral

    • Frailty

    • Open field

Acknowledgement Statement

Every MODEL-AD study should include the following acknowledgment:

The results published here are in whole or in part based on data obtained from the AD Knowledge Portal ( https://adknowledgeportal.synapse.org/ ). The IU/JAX/UCI MODEL-AD Center was established with funding from The National Institute on Aging (U54 AG054345-01 and AG054349). Aging studies are also supported by the Nathan Shock Center of Excellence in the Basic Biology of Aging (NIH P30 AG0380770).

Study Organization

MODEL-AD Studies will be organized in Synapse with a directory schema similar to this:

  • Study_name/

    • Data/

      • Assay_Type_1/ (data from first assay)

      • Assay_Type_2/ (data from second assay)

    • Metadata/

    • Staging/ (data that has yet to be released)

      • Assay_Type_n/ (unreleased data from nth assay)

Best practices for naming data files

Teams should discuss standardizing filenames in working group.

File names should be concise, descriptive, and unique across the entire study. In other words, we should be able to distinguish between each file name and type if there were in one directory. See general file naming recommendations from the Princeton and Stanford libraries.

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