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If you were a member of the lab before the transition to the new online database:
1. Your username should be firstname_lastname, but to verify your username go to our staff about page and find your profile.
2. Click Login in the top right corner of the website.
3. Email slin63@illinois.edu or smideros@illinois.edu for your default password. Use your username and password to login.
4. Change your default password ASAP by going to the password change portion of your profile page.
Please change your password ASAP by going to your profile page.
More info found in sections below.
If you are a new member of the lab:
1. Click "Register" in the top right corner of the website.
2. Fill out the information to register your account.
3. Login using your new account.
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You need to login to access your profile
1. You must first login to edit your profile.
2. Click "Profile" in the top right corner of the website.
3. Click "Edit Profile"
4. Fill out the form and click "Submit Changes"
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1. You must first login to change your password.
2. Click "Profile" in the top right corner of the website.
3. Click "Change Password"
4. Fill out the form and click "Change Password"
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The left bar on the screen holds links that are useful for browsing data.
-Seed Inventory
-IsolateStock Inventory
-Find an Experiment
-Plot Data
-Plant Data
-Samples Data
-Measurement Data
-Query Builder
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Click to access the seed inventory
Searching for a specific Seed ID
1. Enter a Seed ID into the "Search Seed ID" Box
2. Seed IDs which match what you entered are listed below.
3. Click on the Seed ID that matches. This will take you to the Stock Info page, which displays all known information about the seed.
Filtering through Seed Stock Info to find Seed Packets
1. On the Seed Inventory page there are two Filters currently built in: Population and Pedigree
2. Entering a population in the "Select Taxonomy" box causes a list of matching results to appear. You can also click "Show all Populations".
3. Select the checkboxes that meet your needs and click "Select Taxonomies"
4. Entering a pedigree in the "Find a Pedigree" box causes a list of matching results to appear. You can also click "Show all Pedigrees".
5. Select the checkboxes that meet your needs and click "Select Pedigrees"
6. These two filters are applied to the "Seed Stocks" table that appears on the bottom of the Seed Inventory page.
7. You can then select the Seed IDs of interest by selecting the checkboxes, and clicking "Search Inventory for Selected Stocks".
*****IMPORTANT*****
Not all seed stocks have seed packets, and not all seed packets have been inventoried!
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Click to access the isolatestock inventory
Filtering through IsolateStock Info to find Inventoried IsolateStocks
1. On the IsolateStock Inventory page there are two Filters currently built in: Disease Name and binomial
2. Entering a disease name in the "Select Disease" box causes a list of matching results to appear. You can also click "Show all Diseases".
3. Select the checkboxes that meet your needs and click "Select Disease"
4. Entering a binomial in the "Select Taxonomy" box causes a list of matching results to appear. You can also click "Show all Taxonomies".
5. Select the checkboxes that meet your needs and click "Select Taxonomies"
6. These two filters are applied to the "IsolateStocks" table that appears on the bottom of the IsolateStock Inventory page.
7. You can then select the isolatestocks of interest by selecting the checkboxes, and clicking "Search Inventory for Selected IsolateStocks".
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Click to search available experiments
1. A table listing all experiments is shown.
2. You can search using the "Search" box.
3. Click on an Experiment Name to access the Experiment page.
4. The Experiment page holds all datasets that have been recorded for an experiment.
Treatments that were applied to the experiment are listed in a table, or "No Treatment Data" is shown.
Datasets include:
- Seed Planted
- Seed Collected
- Seed Packets Planted
- Seed Packets Collected
- Plant Data
- Plot Data
- Environment Data
- Samples Data
- Measurements Data
5a. By clicking "View" on a dataset, it will take you to a page with the data displayed on a table.
5b. Alternatively, by clicking "Download" on a dataset, a csv file with the data will be downloaded by your browser.
*****IMPORTANT*****
The Experiment page holds all recorded information for a given experiment.
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1. These pages allow you to easily view data sets across different experiments.
2. Enter an experiment name in the "Select Experiments" box, or click "Show all Experiments"
3. Select the experiments you want by clicking the checkboxes, and then click "Select Experiments"
4. You can download the data that is displayed in the table by clicking "Export Data". A csv file will be downloaded by your browser.
*****IMPORTANT*****
If you need more flexibility in browsing data, try using the Query Builder.
If the Query Builder cannot meet your specific needs, write your own custom SQL using PHPMyAdmin.
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Click to access the query builder
The Query Builder allows greater flexibility in querying the database.
1. Select the Data Types you are interested in by clicking the checkboxes.
For Example:
- If you want measurements of row data for an experiment, you would click Measurements, Experiments, and Plots
- If you want measurements that came from seed stocks, you would click Measurements and Seed Stocks
- If you want to know what seed stocks were used in what rows in an experiment, you would click Seed Stocks, Plots, and Experiment
- If you want measurements of row data (and you want to know what seed stocks were planted in those rows), you would click Seed Stocks, Plots, and Measurements
2. Select the field names that you are interested in viewing by clicking their checkboxes.
3. Add any filter sorting options for the fields you selected by selecting a filter from the dropdowns.
4. Add any restrictions to the query for the fields you selected by entering text in the "contains" box.
5a. Click "View Results" to see the results in a table on the website.
5b. Alternatively (and much faster), click "Download Results" to have a csv file with the results downloaded by your browser.
*****IMPORTANT*****
Queries can be quite intensive and slow if the query is very broad. Use the "Download Results" option for faster responses.
If the Query Builder cannot meet your specific needs, write your own custom SQL using PHPMyAdmin.
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1. You must first login to submit a new experiment.
2. Click "New Experiment" in the top header bar.
3. Fill out the form and click "Submit".
4. Your experiment will now show up in "Find an Experiment"
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1. You must first login to submit a new treatment.
2. Click "Add Treatment" in the top header bar.
3. Fill out the form and click "Submit".
4. Your treatment will now show up in Experiment's page.
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1. You must first login to add data.
2. Click "Log Data" in the top header bar.
3. You will see the different data types that are available.
- Download the template that matches the data you want to add.
- Fill in the template with your data.
4. Click "Upload to Queue".
5. Fill out the form and click "Submit".
- Attach the completed template as the file attachment.
*****IMPORTANT*****
When you submit a file using the "Upload to Queue" option, a curator will need to take a look at the file that was submitted, validate it, and then insert the data into the database!
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*****IMPORTANT*****
Ideally all data submitted using the "Upload to Queue" option will be formatted using the templates provided, but it is possible for a curator to work with users to map their data to the templates.
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Click to access the admin page
1. Click on "Django" in the Admin section on the bottom of the left bar.
2. Login to the Admin page. To get admin credentials, contact an administrator.
3. Click "Upload Queues"
4. A list of files and whether the job has been Completed or Not Completed is shown.
5. The curator will then find the files in /data/srv/nelsondb/app/webapp/media/upload_queue/, run validation scripts on the file, and then insert the data into the database.
*****IMPORTANT*****
Validation and data loading scripts still need to be developed.
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