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(-) 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 @@
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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.

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

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

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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.

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Getting Started

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

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Species

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

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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. …

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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

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Populations

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

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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)

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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.

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Samples

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

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Genotype Data

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

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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.

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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.

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Expression Data

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Species

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

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Populations

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

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Samples

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

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Genotype Data

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

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

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