From 82774acb19423672d318fe884d909bfda46bf90d Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 3 Feb 2025 16:06:17 -0600 Subject: Make introductory text more succinct. --- uploader/templates/index.html | 117 ++++++++++++++++++++---------------------- uploader/templates/login.html | 7 +-- 2 files changed, 61 insertions(+), 63 deletions(-) (limited to 'uploader') diff --git a/uploader/templates/index.html b/uploader/templates/index.html index e954a1c..028cbfc 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -10,87 +10,84 @@
{{flash_all_messages()}}
-

Welcome to the GeneNetwork Data Quality Control and Upload System. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.

+

Welcome to the GeneNetwork Data Upload and Quality Control + System.

+

This tool helps you prepare and upload research data to GeneNetwork for + analysis.

-

The sections below provide an overview of what features the menu items on - the left provide to you. Please peruse the information to get a good - big-picture understanding of what the system provides you and how to get - the most out of it.

+

Getting Started

+

The sections below explain the features of the system. Review this guide + to learn how to use the system.

{%block extrapageinfo%}{%endblock%} -

Species

- -

The GeneNetwork service provides datasets and tools for doing genetic - studies — from - - its introduction: - -

-

GeneNetwork is a group of linked data sets and tools used to study - complex networks of genes, molecules, and higher order gene function - and phenotypes. …

-
-

- -

With this in mind, it follows that the data in the system is centered - aroud a variety of species. The species section will - list the currently available species in the system, and give you the - ability to add new ones, if the one you want to work on does not currently - exist on GeneNetwork

- -

Populations

- -

Your studies will probably focus on a particular subset of the entire - species you are interested in – your population.

-

Populations are a way to organise the species data so as to link data to - specific know populations for a particular species, e.g. The BXD - population of mice (Mus musculus)

-

In older GeneNetwork documentation, you might run into the term - InbredSet. Should you run into it, it is a term that we've - deprecated that essentially just means the population.

- -

Samples

- -

These are the samples or individuals (sometimes cases) that were involved - in the experiment, and from whom the data was derived.

- -

Genotype Data

- -

This section will allow you to view and upload the genetic markers for - your species, and the genotype encodings used for your particular - population.

-

While, technically, genetic markers relate to the species in general, and - not to a particular population, the data (allele information) itself - relates to the particular population it was generated from – - specifically, to the actual individuals used in the experiment.

-

This is the reason why the genotype data information comes under the - population, and will check for the prior existence of the related - samples/individuals before attempting an upload of your data.

- -

Expression Data

+

Species

+ +

GeneNetwork supports genetic studies across multiple species (e.g. mice + [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) . + Here you can:

+ + +

Populations

+ +

A "population" refers to a specific subgroup within a species that you’re + studying (e.g., BXD mice). Here you can:

+ + +

Samples

+ +

Manage individual specimens or cases used in your experiments. These + include:

+ + + + +

Genotype Data

+ +

Upload and review genetic markers and allele encodings for your + population. Key details:

+ + + +

Requirement: Samples must already have been registered + in the system before uploading genotype data.

+