EvoNEST Docs

Appearance

Module 5: Data Entry & Management ​

Learning Objectives

By the end of this module, you will have:

  • ✅ Created your first biological sample
  • ✅ Added subsamples (tissues/parts)
  • ✅ Recorded trait measurements
  • ✅ Uploaded files and images
  • ✅ Created experiments with file uploads
  • ✅ Used the data explorer

Estimated Time: 25-35 minutes

Prerequisites ​

Before starting this module, make sure you've completed Module 4: Configuration and have:

  • ✅ Sample and subsample types configured
  • ✅ Trait types with units set up
  • ✅ EvoNEST running and logged in

Overview ​

Now for the practical part - adding real data to EvoNEST! In this hands-on module, you'll learn the complete workflow:

  1. Create a parent sample (an animal specimen)
  2. Add subsamples
  3. Record trait measurements
  4. Create experiments by uploading images
  5. Explore and manage your data

We'll use a practical example you can adapt to your own research.

Exercise: Spider silk research workflow ​

Let's work through a realistic example: documenting a spider specimen and measuring its silk properties.

Scenario: You've collected a garden spider (Araneus diadematus) and want to:

  • Document the specimen
  • Extract silk samples
  • Measure silk diameter

Step 1: Create a parent sample ​

The parent sample represents the whole organism.

1.1 Navigate to Samples ​

  1. Click "Samples" in the main navigation

  2. Click "Add New Sample"

  3. A form will appear

1.2 Fill in General tab ​

The form has multiple tabs. Start with the General tab:

  • Sample Type: Select animal (or your custom type)
  • Notes: (optional) Add any general observations

1.3 Fill in Details tab ​

Click the Details tab:

Collection Information:

  • Responsible: Select admin (your username)
  • Location: Insert any address you like, e.g., Torino Botanical Garden, Italy
  • Latitude: and Longitude: are going to get auto-filled using the address
  • Collection Date: Click calendar icon, select any past date, or leave it as today
  • Parent Sample: Leave blank (this is a parent sample)

Location Helpers

Use the "Use current location" button to auto-fill coordinates, or "Use lab location" to use configured lab coordinates.

1.4 Fill in Animal tab ​

Click the Animal tab for taxonomy:

  • Genus: Araneus
  • Species: diadematus

The form validates taxonomy and auto-fills the family and nomenclature field.

  • Sex: Female

1.6 Review auto-generated name ​

At the bottom of the form, you'll see:

  • Sample Name: Auto-generated as Aradia001 (based on genus + species)

Auto-Generated IDs

The name changes depending on what you set as naming rules in Module 4.

1.7 Submit the sample ​

  1. Review all tabs

  2. Click "Submit" button at the bottom

  3. Success! You should see:

    • Confirmation message
    • The new sample in the samples table
    • A sample ID (e.g., Aradia001)

First Sample Created! 🎉

Congratulations! You've created your first sample in EvoNEST.

Step 2: Create subsamples ​

Subsamples represent parts or derivatives of the parent sample.

2.1 Access Subsample Creation ​

Method 1: From Sample Detail Page

  1. Click on your newly created sample (Aradia001)
  2. Find "Add Subsample" button
  3. Click it

Method 2: From Samples List

  1. Find your sample in the table
  2. Click the "+" or "Add Subsample" action
  3. Form opens

2.2 Create first subsample - dragline silk ​

The subsample form also has tabs. Fill them in order:

General tab:

  • Type: Select silk (from your configured types)

Details tab:

  • Responsible: admin (auto-filled)
  • Location: Use any address, or lab location
  • Date: Leave it as today or edit it
  • Parent Sample: Select Aradia001

When you select the parent, taxonomy fields auto-fill.

Subsample tab:

  • Subsample Type: write dragline (from your configured types)
  • Include Subsample Shortened: Check this to add subsample type code to the name
  • Box: 1
  • Slot: 1

The Name field at the bottom auto-generates as Aradia001_dl001 (with dragline shortcode dl).

Click "Submit" to save.

2.3 Create second subsample of the same type ​

If you now press again Submit, you can create a second subsample of the same type. The name should auto-generate as Aradia001_dl002.

  1. Click "Submit"

Multiple Subsamples

You can create as many subsamples as needed from one parent:

  • Different tissues (muscle, bone, organs)
  • Different silk types (dragline, capture spiral, egg sac)
  • Replicates (multiple extractions)
  • Time series (samples at different dates)

Verify subsamples ​

  1. Click on the parent sample name (Aradia001)

  2. You should see:

    • A detailed page with all the sample info
    • On the right, a list of associated subsamples

Step 3: Record trait measurements ​

Now let's add measurements for your silk samples.

3.1 Navigate to Traits ​

  1. Click "Traits" in the main navigation

  2. Click "Add Trait" or "Record Measurement"

3.2 Record fibre diameter ​

The trait form is organized in tabs. Let's fill them:

General tab:

  • Trait Type: Select diameter
  • Equipment: Select light_microscope (or add custom equipment)

Details tab:

  • User: admin (auto-filled)
  • Date of measurement: Today

Values tab:

  • Sample: Select Aradia001_dl001 (the dragline silk subsample)
  • Detail of the sample measured: all or mid-section
  • Measurements: Enter replicate values (separate them via comma):
    3.1, 3.3, 3.2, 3.4, 3.0
  • Unit: μm

EvoNEST automatically calculates:

  • Mean: 3.2 μm
  • Standard Deviation: 0.15 μm

Click "Submit" to save.

3.3 Record tensile strength ​

  1. Click "Add Trait" again

  2. Fill in the tabs:

    General tab:

    • Trait Type: tensile_strength
    • Equipment: t150_utm

    Details tab:

    • Date: Today

    Values tab:

    • Sample: Aradia001_dl001
    • Detail: single fibre
    • Measurements: 1100 (or list: 1100, 1050, 1150)
    • Unit: MPa

  3. Click "Submit"

Step 4: Create an experiment with images ​

In EvoNEST, experiments are created by uploading files (images, documents, or data files) and linking them to samples.

Experiments and Data Parsing

Advanced Feature: EvoNEST can automatically parse data files (CSV, XLSX, instrument outputs) to extract trait measurements. When you upload structured data files, custom parsers can:

  • Automatically extract measurements
  • Create trait entries
  • Link data to samples
  • Generate statistics

In this tutorial, we'll use simple image uploads to learn the basics. If you're interested in creating custom parsers for your instrument data, see the Data Format Parser Development Guide and File Processor Development Guide after completing the tutorial.

4.1 Download practice images ​

Let's use real images for this exercise:

  1. Download the spider specimen photo:

  2. Download the silk microscopy image:

4.2 Navigate to Experiments ​

  1. Click "Experiments" in the main navigation

  2. Click "Add Experiment" or "New Experiment"

  3. The experiment form opens with tabs

4.3 Upload specimen image as experiment ​

Let's create our first experiment - the specimen documentation.

General tab:

  1. Responsible: admin (auto-filled)

  2. Import file: Click or drag-and-drop the Aradia001_specimen.jpg image

  3. Experiment Type: Select image

    • EvoNEST automatically detects it's an image file

  4. Experiment Name: Aradia001 - Specimen Photo

  5. Optional notes:

    Adult female Araneus diadematus specimen. 
Collected from University Botanical Garden.

Details tab:

  1. Sample: Select Aradia001 (your parent sample)
    • This links the image to the specimen

Image tab (appears when type is "image"):

  • Shows preview of your uploaded image
  • Sample Name: Should show Aradia001 (auto-linked)

Click "Submit" - Your first experiment is created!

What Are Experiments?

Experiments in EvoNEST store and organize research files:

Basic file storage (this tutorial):

  • Images (specimen photos, microscopy, etc.)
  • Documents (protocols, notes, reports)
  • Linked to samples for organization

Advanced data parsing (optional):

  • Upload structured data files (CSV, XLSX, instrument outputs)
  • Automatic trait extraction via custom parsers
  • Measurements automatically linked to samples
  • Statistical analysis of parsed data

For simple documentation (images, PDFs), experiments work as file containers. For instrument data and measurements, you can develop custom parsers to automate trait extraction. See Technical Documentation to learn more.

4.4 Create a second experiment - silk microscopy ​

Now let's add the silk SEM image:

  1. Click "Add Experiment" again

  2. General tab:

    • Import file: Upload Aradia001_silk_SEM.jpg
    • Experiment Type: image
    • Experiment Name: Aradia001_dl001 - Silk SEM Microscopy
    • Notes: SEM image of dragline silk at 2000x magnification

  3. Details tab:

    • Sample: Select Aradia001_dl001 (the dragline silk subsample)

  4. Click "Submit"

4.5 View your experiments ​

  1. Go to "Experiments" in the main navigation

  2. You should see your two image experiments listed

  3. Click on an experiment to view:

    • The full image
    • Linked sample information
    • Upload date and responsible user
    • Any notes you added

Step 5: Explore your data ​

Learn to find and filter your data.

5.1 Explore samples ​

  1. Go to "Samples" → "Animal"

  2. Try the table filters:

    • Family: Type Araneidae → See only spider family
    • Type: Select animal → Filter by sample type
    • Date Range: Select this month → Recent samples
    • Responsible: Select your name → Your samples only

  3. Search:

    • Type Araneus in search box
    • See matching samples

  4. Sort:

    • Click column headers to sort
    • Click again to reverse order

5.2 Explore traits ​

  1. Go to "Traits" → "Analysis"

  2. Select Trait "Fibre Diameter"

  3. View statistics:

    • Min, max, mean, std dev (if configured)

Step 6: Edit and update data ​

Learn to modify existing entries.

Edit a sample ​

  1. Go to the Animal table or the General table of Samples → Find Aradia001

  2. Click the sample name to open the sample page

  3. Make changes in the relevant tabs:

    • Update notes
    • Set the life stage of the animal
    • Correct taxonomy in Animal tab

  4. Check logbook:

    • EvoNEST tracks all changes
    • View change history in the logbook section

Edit a trait ​

  1. In the same page, click the button "See Sample Traits"

  2. Make changes directly in the table:

Data Integrity

EvoNEST maintains a logbook (change history) for all edits:

  • Who made the change
  • When it was changed
  • What was changed

This ensures transparency and traceability of your data.

Practice exercises ​

Now it's your turn! Practice by adding more data:

Exercise 1: Add another specimen ​

Create a second spider sample:

  • Different species (e.g., Latrodectus hesperus)
  • With subsamples
  • With measurements
  • Upload a specimen photo as an experiment

Exercise 2: Time series data ​

Add measurements over time:

  • Day 1: Initial diameter measurement
  • Day 7: After conditioning
  • Day 14: After stress testing

(Use same sample, different dates)

Exercise 3: Multiple images ​

For one subsample, upload:

  • Light microscopy image (experiment)
  • SEM image (experiment)
  • Field photo (experiment)
  • Link all to the same sample

Checkpoint: Data entry complete? ​

Before moving to the next module, verify:

Data entry skills achieved!

You now have the core skills to use EvoNEST for your research data management!

Ready for advanced features? If you work with instrument data files (tensile testers, spectroscopy, chromatography, etc.), you can create custom parsers to automatically extract measurements from data files. See:

Next steps ​

Congratulations on completing the data entry module! You now know how to manage research data in EvoNEST.

Continue learning ​

Released under the AGPL License.