DARE User Guide

What the builder does

The DARE Template Builder (link in the sidebar) turns your experiment plan into the files DARE needs, and checks your data before you submit it. Once all the fields are filled in, the builder will produce two CSV files, named after your taxon and surname:

File	What it holds	When you send it
`DARE_<taxon>_<surname>_metadata.csv`	Everything you enter in the form: organism, site, medium, design and measurements	Before the experiment, with the signed author agreement, to get a study ID
`DARE_<taxon>_<surname>_data.csv`	One row per measurement with the IDs filled in; you add your study ID, dates and values	After the experiment

The submission process

You need a study ID before you start the experiment. These IDs will be provided by the organizers after your experimental design is approved.

Fill in the template builder and download the two files.
Read and sign the author agreement.
Upload the signed author agreement and your metadata file from the builder’s Submit page.
The core team reviews your design.
Once approved, you will receive a confirmation and your study ID.
Run the experiment. Copy your study ID into every row of the data file and fill in your measurements.
Check the data file in the builder, then upload it from the Submit page.

Before you start

One submission covers one species from one collection site. Several clones from the same site stay in one submission, but other species, or populations from other sites, should each get their own submission (see Several species or populations).
Gather your details first. The Template Fields page names every field in the builder, with units and which are optional: DARE Template Field List
Open the Template Builder. Click Load example to see a completed form for Daphnia magna.

Protocol requirements at a glance

The builder checks your form, but several protocol requirements are about how you run the experiment. This summary is taken from the DARE protocol, which has the full details and the reasoning behind them.

Topic	What the protocol asks
Organism	An organism you know well, recently isolated from the field (as a rough guide, within 1–2 years). If you use a culture already in your lab, judge whether it still represents the natural population. Contact the core team before using an organism if you don’t have environmental data recorded from when it was collected.
Field data	Isolate during the growing season if you can. Record at least the exact location, water temperature, and salinity or conductivity, plus any further chemistry you have.
Medium	A medium that supports normal growth, development and survival under ambient conditions. Use the same base medium in every treatment, with only temperature or salinity changed, and document any modification.
Feeding	Report whether, how often and with what the organism is fed during the experiment.
Temperature	Ambient is the average growing-season temperature; elevated is ambient + 4 °C. Keep treatments stable, expose organisms continuously for the whole experiment, minimize and document fluctuations, and record the temperatures organisms actually experience.
Salinity	Ambient is the salinity at the collection site (natural or filtered water) or of the culture medium (artificial medium). Freshwater: 2× ambient, made with NaCl. Marine: 5 PSU below ambient by default, but this can be altered in discussion with the organizers. Brackish: the direction and size of the change are up to you. Contact the core team before using a salt other than NaCl. Measure salinity at the start and end, and preferably throughout.
Replication	One experimental replicate with at least 3 vessels (technical replicates) per treatment (4–5 preferred), or more if your organism calls for it.
Responses	At least one performance response: population growth, somatic growth, body size, development time, reproduction, survival or activity. Physiological traits are welcome in addition. Contact the core team before using another performance measure. Choose traits you can measure reliably throughout the experiment.
Duration and sampling	Long enough for a measurable response, justified by your organism’s biology. Measure at the start (T0, unless no initial measurement is needed) and the end (Te), and in between where feasible: daily or several times per generation for fast-growing organisms, weekly or at developmental stages for slower ones.

Filling in the form

Work through the six sections in the left-hand list. Each one shows done or a count of items to fix, and a message under each field explains any problem.

Study and contact: contact details, country, data origin, level of organization (population or individual), and whether the organism was newly isolated or is already in culture.
Organism and field site: taxon, ecosystem, collection date, coordinates in decimal degrees, water temperature, and salinity with its unit. Air temperature, dissolved oxygen and further water chemistry are optional. The collection date should be no more than 1–2 years before the experiment.
Culture history (only shown for organisms already in culture): generations in the lab, culture temperature, feeding regime, light:dark cycle, and light intensity for photosynthetic organisms.
Experimental medium: use the same base medium in every treatment and describe any modification.
Design and treatments:
- Choose the design and enter the ambient temperature. The elevated temperature is ambient + 4 °C. Contact the core team before using a different increase. Extra temperature levels use the same step.
- Enter the ambient salinity. The stress level is added automatically: twice ambient for freshwater organisms and -5 psu for marine organisms (the size of the decrease is up to each lab). For brackish organisms, you choose the direction and size of the change. Further levels are optional.
- Check the list of treatments and enter the salt added to each, or the water added for a decrease.
- Describe feeding during the experiment.
- Set the replication. A schematic under the treatment list shows how it fits together:
  - Experimental replicates: how many times you run the whole experiment. Leave it at 1 unless you plan on repeating the whole set of exposures multiple times.
  - Vessels per treatment (technical replicates): at least 3, with 4–5 preferred.
  - Individuals per vessel and individuals measured per vessel, for individual-level experiments.
Measurements and sampling:
- Add one measurement type for each thing you record. Record the raw quantity, such as fluorescence or body length, rather than a calculated rate.
- For each one, give the response it informs, a method description, the unit, how many measurements you take per individual (or per vessel), whether higher means better performance, and when initial measurements are made. Choose No initial measurement needed where a starting value isn’t meaningful, such as egg counts.
- Enter the proposed start date and the planned sampling days. Start with day 0 (T0) if any measurement type has an initial measurement; otherwise start with your first sampling day.
- Choose whether measured temperature and salinity are recorded per treatment or per vessel.

Exporting the two files

Open Export templates and download both files, then go to Submit to send the metadata file with the signed author agreement.

Missing items: the box at the top lists anything still to fix. Click a section name to jump to it.
Treatments: the treatments table shows what the data file will contain. Check it before downloading.
Drafts: you can download a draft at any time. Open issues are noted inside the metadata file.
If Download does nothing: use Show contents to copy the text instead.

Filling in the data file

Once your design is approved, open the data file in any spreadsheet program and fill in these columns. Rows are sorted by time point, so each sampling day is one block.

Column	What to enter
`study_id`	Your study ID from the core team, in every row
`date`	The actual measurement date, as YYYY-MM-DD
`time`	24-hour HH:MM, or leave empty
`elapsed_days`	Days since T0
`value`	A number with a decimal point, in the units given in the metadata. Write NA if a value is missing.
`qc_flag`	ok, suspect, below_detection, or empty
`notes`	Free text, including the reason for any NA

Don’t edit the other ID and target columns, and don’t delete rows. To add an unplanned time point, copy an existing row.
Vessels and individuals: vessel_id names each vessel (for example T20_S620_V3) and individual_id each measured individual (T20_S620_V3_I2). experimental_rep is 1 unless you repeat the whole experiment.
Readings: rows with reading 2, 3… are repeated measurements of the same individual or sample.
Survival: recorded once per vessel, as the proportion alive.
Measured conditions: rows named realized_temp_c and realized_conductivity (or realized_salinity) are for the temperature and salinity you measured. Record them at least at the start and end of the experiment, and preferably throughout.
Saving: save as CSV UTF-8 (comma delimited). In Excel, choose this under Save As. LibreOffice, Numbers and Google Sheets use UTF-8 by default.
Dates: spreadsheets sometimes reformat dates when saving. To prevent this, format the date column as text before typing.

Checking the data file

It will help the lead team if you are able to run every data file through the checker before you submit it.

Open Check a data file and drop in the data CSV. Add the metadata CSV in the same drop if it is not the one currently loaded in the form.
Read the report. Error items should be fixed before submission. Check items are worth a look. Each item gives the row numbers involved.
Fix the problems in your spreadsheet, save, and drop the file in again.
When there are no errors, upload the data file from the Submit page, together with the metadata file if anything changed since approval.

The most common errors are semicolon separators, decimal commas, dates written as day/month, edited ID columns, and fewer than 3 vessels per treatment with data at the end. An empty study_id column gives a warning until you add your study ID. Try it on a simulated file shows an example report.

Several species or populations

Each species or population is a separate submission, with its own metadata file and study ID. The builder copies the shared details so you don’t retype them.

Finish the first submission and click Save progress.
Click Start another species, then click it again to confirm. If the current form hasn’t been saved, the button warns you first.
Fill in the organism, site and culture history for the new species.

The button copies the contact details, medium, design, measurement types and sampling plan. It clears the organism, site and culture history, and adds the previous species to Related submissions. If several species share a vessel, contact the core team before starting.

Saving and coming back later

Your metadata file is your save. The browser keeps only one draft, and it can be lost.

Save progress: the button at the top downloads your metadata file at any point, finished or not. Keep it somewhere safe.
Continue later: open the builder, click Open saved metadata… and choose the file. Everything you entered comes back, including treatments and measurement types.
Changing an approved design: open your metadata file, make the change, save it and send it to the core team again.
Browser draft: the page also saves a draft automatically, in the same browser on the same computer only. It is lost if browser data is cleared or you use a private window.
Clear form: click it twice to start over.

Troubleshooting

Problem	Fix
Download button does nothing	Click Show contents, paste the text into a text editor, and save it with the file name shown.
The spreadsheet puts all the data in one column	Import it as comma-separated. In Excel, use Data > From Text/CSV.
The checker says the columns are separated by semicolons, or warns about the text encoding	Save the file again as CSV UTF-8 (comma delimited).
Dates are flagged	Format the date column as text and retype the dates as YYYY-MM-DD.
The page looks plainer when offline	The fonts load from the internet. Everything else works the same.