What Your AI Assistant Can Do

This page lists everything your AI assistant can do in Conspecta, grouped by workspace. Each of its 150 rows is one action, such as reading a sample or adding rows to a table.

A connection or key with Read only access gets the 82 actions marked Read only. The other 68 need Read and write. Connect your AI assistant covers connecting and choosing the access.

Most assistants show the name in code under each action, such as update_task, when they use it or ask your permission to.

Your assistant looks up sequences in NCBI or UniProt through 4 actions, and nothing about you, your lab or your project goes with them. Another 5 run work on a server and draw on your team's compute usage. The Access column marks both kinds.

Projects and Search

Your assistant works in one project at a time, and its searches can reach every project you can open.

Action	What it does	Access
List your projects `list_projects`	Lists the projects you can open, newest first.	Read only
Read a project `get_project`	Reads one project, including your role on it.	Read only
Search everything `search_global`	Searches samples, notes, tables, image analysis, figures, contacts and more together, in one project or across all of yours.	Read only
See what changed lately `recent`	Lists the records changed most recently, across every kind of record.	Read only
Search this guide `search_guide`	Finds the passages of this guide that answer a question about how Conspecta works, with a link to each.	Read only
Star a record `star_resource`	Stars a record for you, so it appears with your starred items.	Read and write
Remove a star `unstar_resource`	Takes your star off a record.	Read and write

Samples

The samples in a project and the sample groups that hold them. Track your samples covers both.

Action	What it does	Access
List samples `list_samples`	Lists the samples in a project, newest first.	Read only
Read a sample `get_sample`	Reads one sample with all of its details.	Read only
Search samples `search_samples`	Finds samples by any words in them.	Read only
Register a sample `create_sample`	Adds a sample with its name, type and descriptive details, and leaves its measurements for you to record in the app.	Read and write
Edit a sample `update_sample`	Changes a sample's name, description, external ID, species, strain, status or tags.	Read and write
Create a sample group `create_sample_set`	Makes a named sample group, with any samples you name already in it.	Read and write
Add samples to a group `add_to_sample_set`	Adds samples to a sample group and reports any it skipped.	Read and write

Notebook

Notes and protocols share the notebook. Write lab notes covers the pages themselves.

Action	What it does	Access
List notebook pages `list_notebook_pages`	Lists the notes and protocols in a project by title, or only one kind.	Read only
Read a notebook page `get_notebook_page`	Reads a note or protocol in full, including a protocol another team shared with yours.	Read only
Search notebook pages `search_notebook_pages`	Finds notes and protocols by any words in them.	Read only
Write a notebook page `create_notebook_page`	Writes a new note or protocol, saved as a draft for you to review and sign off.	Read and write
Add to a notebook page `append_to_notebook_page`	Adds text or protocol steps to the end of a page and leaves the rest as it was.	Read and write
Rewrite a passage `edit_notebook_page`	Replaces or deletes one passage on a page and leaves the rest of the page as it was.	Read and write
Rename or move a notebook page `update_notebook_page`	Renames a page, moves it to another folder, or turns a note into a protocol or back.	Read and write

Protocols

Running a protocol step by step and reading its results. Run a protocol covers the bench side.

Action	What it does	Access
Read a protocol's steps `list_protocol_steps`	Reads a protocol's steps in order, with what each one measures, the reagents it uses, its hazards and where it branches.	Read only
List protocol runs `list_protocol_runs`	Lists the runs of one protocol, or every run in the project, such as the ones still in progress.	Read only
Read a protocol run `get_protocol_run`	Reads one run with its status and scale.	Read only
Read a run's checked steps `list_protocol_run_steps`	Lists the steps checked off in a run, with any notes and deviations.	Read only
Read every run's results `get_protocol_results`	Reads every run of a protocol together, with the values recorded in each run and the rows of its result tables.	Read only
Start a protocol run `start_protocol_run`	Starts a new run of a protocol in this project.	Read and write
Check off a step `mark_protocol_step`	Checks a step on or off in a run and records its measurements, a note, a deviation, or which way a branch went.	Read and write
Pause, complete or abandon a run `update_protocol_run`	Changes a run's status or scale, and completes it once every required measurement is filled in.	Read and write

Data Tables

Tables of your own and cytometry panels, which are tables too. Data tables covers the grid.

Action	What it does	Access
List data tables `list_tables`	Lists a project's data tables and panels with their columns and row counts.	Read only
Read table rows `get_table_rows`	Reads the rows of a data table, with each formula and the value it gives.	Read only
Create a data table `create_data_table`	Creates an empty table with the columns you name, or a new cytometry panel.	Read and write
Add rows `add_table_rows`	Adds rows to the end of a table and leaves the rows already there as they were.	Read and write
Change cells `update_table_rows`	Changes the cells you name in rows a table already has and leaves every other cell as it was.	Read and write
Rename a table `rename_data_table`	Renames a data table or a panel, with its rows, folder and links unchanged.	Read and write

Figures

Composing figures from your images, charts and text. Figures covers the editor.

Action	What it does	Access
List figures `list_figures`	Lists a project's figures and their folders.	Read only
Read a figure `get_figure`	Reads a figure's layout, lettering, status and what each panel shows.	Read only
List figure layouts and styles `list_figure_options`	Lists the layouts, canvas shapes, lettering styles and chart types the figure editor offers.	Read only
List charts for a figure `list_figure_chart_sources`	Lists the charts you can put on a figure panel from an image analysis, a flow cytometry analysis or a data table.	Read only
Compose a figure `create_figure`	Lays out images, charts and text panels as a new figure, saved as a draft.	Read and write
Change a figure `update_figure`	Renames a figure, changes its layout or status, or changes, adds or replaces panels, and leaves the panels you didn't name as they were.	Read and write

Planner

Cards on a project's board and calendar. Plan your experiments covers the board.

Action	What it does	Access
List cards `list_tasks`	Lists the cards on a project's board, with the board's columns and tags.	Read only
Read a card `get_task`	Reads one card in full, with the names of its tags and its repeat schedule.	Read only
Search cards `search_tasks`	Finds cards by any words in them.	Read only
List board tags `list_task_tags`	Lists every tag on a board, including tags not yet on any card.	Read only
Add a card `create_task`	Adds a card to the column you choose, with its tags, dates, repeat and the cards that have to finish first.	Read and write
Change a card `update_task`	Moves a card between columns or changes its title, details, tags, priority or dates.	Read and write
Create a board tag `create_task_tag`	Adds a new tag to the board, ready to put on cards.	Read and write

Images

Microscopy image sets and the photos attached to your records. Image viewing covers the viewer.

Action	What it does	Access
List microscopy image sets `list_image_sets`	Lists the microscopy image sets attached to a sample, an image analysis or another record.	Read only
Read an image set `get_image_set`	Reads a microscopy image set with each series' size, bit depth, channels, z-slices and timepoints.	Read only
List images `list_images`	Lists the photos and other images attached to a record.	Read only
Read an image's details `get_image`	Reads an image's filename, dimensions and capture time.	Read only

Image Analysis

Measuring images and checking the result before it is saved. Analyze images covers the workspace.

Action	What it does	Access
List image analysis `list_image_analyses`	Lists every image analysis in a project, each with its newest run.	Read only
Read an image analysis `get_image_analysis`	Reads one image analysis with its runs, result numbers and the tables it produced.	Read only
List ready-made methods `list_image_analysis_presets`	Lists the ready-to-run image analysis methods the app offers, such as counting cells or measuring colocalization.	Read only
List image analysis settings `list_image_analysis_settings`	Lists every setting a step can take, with what it does, its range and its default.	Read only
Set up an image analysis `create_image_analysis`	Creates an image analysis over existing images from a method, a ready-made one or a template, ready to run.	Read and write
Run an image analysis `run_image_analysis`	Runs an image analysis method over images and returns the counts and measurements for each image.	Read and write Draws on your team's compute usage
Check a run `get_image_analysis_qc`	Reads a run back with its exact steps, the settings used on each image, the objects its filters kept and dropped, and its quality flags.	Read only
Look at what a run detected `view_image_analysis_detections`	Shows an image with every detected object outlined, the objects one by one with their sizes and positions, or the ones a filter dropped and why.	Read only
Save a run's results `write_image_analysis_results`	Saves a finished run's numbers into an image analysis, or recounts them under new filters without detecting anything again.	Read and write
Run an image analysis over a set `run_image_analysis_batch`	Runs an image analysis over a set of images on a server, neural-network detectors included, and saves the rows into the image analysis when it finishes.	Read and write Draws on your team's compute usage
Follow a run over a set `get_image_analysis_batch`	Reads how a run over a set is going, and each image's results once it finishes.	Read only
Try a range of values for a setting `sweep_image_analysis_setting`	Reruns a recorded run across a range of values for one setting and reports the number each value gives, saving nothing.	Read and write Draws on your team's compute usage, except when the setting is a filter
Ask for a review `request_image_analysis_review`	Asks project members, by email address, to review a shared image analysis.	Read and write

Image Analysis Templates

The lab's saved ways of measuring images. Image analysis templates covers versions and pipeline files.

Action	What it does	Access
List image analysis templates `list_image_analysis_templates`	Lists a project's templates with their versions and how many times each has been used.	Read only
Read an image analysis template `get_image_analysis_template`	Reads a template's steps, settings and kept versions.	Read only
Find the image analysis built from a template `list_image_analysis_template_analyses`	Lists every image analysis built from a template and marks the ones made from an older version.	Read only
Export a pipeline file `export_image_analysis_template`	Writes one version of a template as a pipeline file you can share with another lab or keep with a paper.	Read only
Save a template `create_image_analysis_template`	Saves an image analysis as a new template in the project's library.	Read and write
Publish a template's next version `update_image_analysis_template`	Publishes an image analysis's steps and settings as a template's next version, with every earlier version still in its history.	Read and write
Import a pipeline file `import_image_analysis_template`	Adds a pipeline file to the project's library as a new template, after showing you what it holds.	Read and write

Flow Cytometry

FCS files, gating and the numbers from them. Analyze flow cytometry covers the workspace.

Action	What it does	Access
List flow cytometry analysis `list_flow_analyses`	Lists every flow cytometry analysis in a project, with how many gates each has.	Read only
Read a flow cytometry analysis `get_flow_analysis`	Reads a flow cytometry analysis with its gates, their parents and the channels each was drawn on.	Read only
List FCS files `list_fcs_files`	Lists a project's FCS files with their cytometer, event count and acquisition time, newest first.	Read only
Read an FCS file's details `get_fcs_file`	Reads one FCS file's record, including the analysis and gate it was saved from.	Read only
List gating templates `list_gating_templates`	Lists a project's gating templates with their versions and gate counts.	Read only
Read a gating template `get_gating_template`	Reads a gating template's gates and the channels its compensation covers.	Read only
Find the flow analysis built from a template `list_template_analyses`	Lists every flow cytometry analysis built from a gating template and marks the ones made from an older version.	Read only
Start a flow cytometry analysis `create_flow_analysis`	Creates a flow cytometry analysis over FCS files, with no gates yet.	Read and write
Apply a gating template `apply_gating_template`	Applies a saved gating strategy to a set of FCS files as a new flow cytometry analysis, fitting each gate to each file's own channels.	Read and write
Count populations `compute_flow_statistics`	Counts a flow cytometry analysis's populations across its files and returns the counts and percentages.	Read and write Draws on your team's compute usage
Save population counts `write_flow_statistics`	Saves a finished count into the flow cytometry analysis's results table.	Read and write
Cluster files `run_flow_clustering`	Runs clustering or dimensionality reduction on one file, or several pooled together, on a server.	Read and write Draws on your team's compute usage
Read a clustering run `get_flow_clustering_run`	Reads how a clustering run is going, and once it finishes, how many populations it found and the events in each.	Read only
Save a clustering run `write_flow_clustering`	Saves a finished clustering run onto its flow cytometry analysis, in place of the one saved before.	Read and write

Panel Design

Choosing markers and dyes for a cytometer. Design a panel covers the panel page.

Action	What it does	Access
List fluorochromes `list_dyes`	Lists the fluorochromes the dye picker offers, with their peaks and which ones the lab has in stock.	Read only
List markers `list_markers`	Lists the markers suggested on the panel sheet, each with a note on what it reports.	Read only
List measured dyes `list_dye_signatures`	Lists the dyes the lab has measured on one cytometer from single-stain controls.	Read only
Score a panel `score_panel`	Scores how alike each pair of dyes looks on a cytometer, the same check the panel page shows.	Read and write
Set a panel's cytometer `set_panel_instrument`	Sets which of the lab's cytometers a panel is designed for, or clears it.	Read and write
Record a cytometer's optics `set_instrument_optics`	Records the published lasers and detectors for a cytometer's model, so its panels can be scored.	Read and write

Sequences

Plasmids, primers, genes and constructs, and the public databases behind them. Manage sequences covers the registry.

Action	What it does	Access
List sequences `list_genetics`	Lists a project's plasmids, primers, genes and constructs with their length and GC content.	Read only
Read a sequence's details `get_genetics_item`	Reads a sequence record's details and length.	Read only
Read a sequence's bases `get_sequence`	Reads the bases of a sequence, or any stretch of it, numbered from base 1 as the viewer numbers them.	Read only
Find a stretch of bases `search_sequences`	Finds which of your sequences contain an exact stretch of bases, on either strand.	Read only
Register a sequence `create_genetics_item`	Adds a plasmid, primer, gene or other sequence from bases you give it.	Read and write
Edit a sequence record `update_genetics_item`	Changes a sequence record's name, description, source or tags.	Read and write
Mark a region `annotate_genetics_item`	Marks and names regions on a sequence's map, and the regions already on it stay in place.	Read and write
Search NCBI and UniProt `search_ncbi`	Searches NCBI and UniProt for published sequences by gene, organism or accession.	Read only Sends your search words to NCBI or UniProt
Add a published sequence `fetch_accession`	Files a published sequence in your library from its accession, with the accession recorded on it.	Read and write Sends the accession to NCBI or UniProt
Run a BLAST search `run_blast`	Searches NCBI for sequences like the one you give it, to identify an unknown band, read or construct.	Read and write Sends the sequence to NCBI
Read a BLAST search `get_blast`	Reads a BLAST search's progress and, once it finishes, its matches.	Read only Reads the result from NCBI

Inventory and Orders

Reagents, consumables and kits, and the orders that restock them. Reagent inventory covers stock.

Action	What it does	Access
List stock `list_inventory`	Lists a project's reagents, consumables and kits with quantity, reorder point, storage, supplier and expiration.	Read only
Read a stock item `get_inventory_item`	Reads one item with its quantity and reorder levels, and the dye, clone, host and reactivity of an antibody.	Read only
Add a stock item `create_inventory_item`	Adds a reagent, consumable or kit with its quantity and storage.	Read and write
Change a stock item `update_inventory_item`	Changes an item's quantity, storage, supplier or status.	Read and write
List orders `list_orders`	Lists a project's orders with their status, cost, urgency and supplier.	Read only
Read an order `get_order`	Reads one order in full.	Read only
Record an order `create_order`	Records a purchase order for an item and its quantity.	Read and write
Update an order `update_order`	Moves an order along its statuses, such as marking it received, or changes its details.	Read and write

Storage and Instruments

The lab's freezers, shelves and boxes, and the instruments it books. These belong to the lab, so a change reaches every project. Lab storage and instruments covers both.

Action	What it does	Access
List storage and instruments `list_locations`	Lists the lab's freezers, shelves, boxes and bookable instruments, including instruments other teams share with yours.	Read only
Read a location `get_location`	Reads one storage location or instrument, including an instrument's recorded optics.	Read only
Add a storage location `create_location`	Adds a freezer, shelf, box or other storage location to the lab.	Read and write
Change a storage location `update_location`	Changes a location's name, type, description or status.	Read and write
Read an instrument's schedule `get_instrument_schedule`	Reads an instrument's booking rules, bookings, downtime and notices.	Read only
Book an instrument `book_instrument`	Books time on one of the lab's instruments, or on one another team lets yours book, within its rules.	Read and write

Well Plates

Saved plate layouts and the plates laid out from them. Well plates covers plates.

Action	What it does	Access
List plate templates `list_plate_templates`	Lists a project's plate templates with their plate format, configured wells and version.	Read only
Read a plate template `get_plate_template`	Reads a plate template's layout well by well, with each well's group, label, concentration and volume.	Read only
Find the plates built from a template `list_plate_template_plates`	Lists the plates built from a plate template and marks the ones laid out before its latest change.	Read only

Contacts

The people and organizations the lab deals with, and its log of calls, emails and meetings. Keep contacts and a log covers both.

Action	What it does	Access
List contacts `list_contacts`	Lists the lab's people or its organizations, searched, sorted and filtered by tag, follow-up day, where you stand with them and more.	Read only
Read a contact `get_contact`	Reads one person or organization, with their organizations, last contact and follow-up day.	Read only
Find a contact by email or ID `find_contacts`	Finds a person by a whole email address, or anyone by an outside identifier such as an ORCID iD.	Read only
Read a contact's links `get_contact_links`	Lists the organizations a person belongs to, or an organization's people and the organizations it is part of or affiliated with.	Read only
Read the contact log `list_log_entries`	Reads the lab's logged calls, emails, meetings and notes, for everyone or one contact, narrowed by kind, direction, author or days.	Read only
List sources `list_sources`	Lists the places the lab's contact details come from, such as a staff directory, and any marked unreliable.	Read only
List contact tags `list_contact_tags`	Lists the lab's contact tags with how many people and organizations have each.	Read only
List contact fields `list_contact_fields`	Lists the extra fields the lab keeps on people and organizations.	Read only
Add a contact `create_contact`	Adds a person or an organization to the lab's Contacts.	Read and write
Edit a contact `update_contact`	Changes the fields you name on a person or an organization, including their primary organization and the Do not contact mark.	Read and write
Load a list of contacts `upsert_contacts`	Loads up to 100 people or organizations at a time, matched by email address or identifier, so loading the same list twice adds nobody twice.	Read and write
Log a contact `add_log_entry`	Logs a call, email, meeting or note with a person or an organization.	Read and write
Correct a log entry `update_log_entry`	Corrects a log entry's kind, direction, text, day or time.	Read and write
Link contacts `link_contacts`	Records that a person belongs to an organization, or that one organization is part of or affiliated with another.	Read and write
Change a link between contacts `update_contact_link`	Changes a membership's role, dates, primary organization or main contact, or where a link came from.	Read and write
Remove a link between contacts `unlink_contacts`	Removes a membership or a link between organizations, and both contacts stay in Contacts.	Read and write
Add or change a source `save_source`	Adds a source of contact details, or renames one or marks it unreliable.	Read and write
Mark a value wrong `mark_value_wrong`	Marks a contact's value wrong when you say it is, so no edit or load can set it again.	Read and write
Add or change a contact tag `save_contact_tag`	Adds a contact tag, or renames or recolors one everywhere it is used.	Read and write
Define a contact field `save_contact_field`	Defines a field the lab keeps on people or organizations, or renames, changes or archives one.	Read and write

Comments, Reviews and History

Comments work on most records, from samples and sequences to orders and planner cards. Sign-off covers notebook pages, sequences, figures, data tables, image analysis, flow cytometry analysis, samples, orders, protocol runs, gating and plate templates, and single images. Review and share notes covers signing off a notebook page.

Action	What it does	Access
Read comments `list_comments`	Reads the comments on a record, oldest first, with who wrote each and when.	Read only
Leave a comment `add_comment`	Leaves a comment on a record under your name, and notifies anyone mentioned in it.	Read and write
Read a record's sign-offs `list_approvals`	Reads whether a record is signed off and every decision recorded on it.	Read only
Summarize reviews `get_review_summary`	Summarizes a workspace's sign-offs, which records changed since, and who still has a review to do.	Read only
Read history `get_activity`	Reads who changed what and when, for a whole project or one record.	Read only

Links Between Records

The links that tie a sample to its images, results and notes. How your work connects covers them.

Action	What it does	Access
Read a record's connections `get_connections`	Lists the records linked to one record, such as a sample's images, image analysis and notebook pages.	Read only
Link two records `link_resources`	Records that two records in a project are connected, such as an image analysis made from a sample.	Read and write
Remove a link between records `unlink_resources`	Removes a link between two records.	Read and write

Records From Other Teams

Panels, templates and protocols other teams in your organization shared with yours. Share and export covers sharing.

Action	What it does	Access
List records from other teams `list_records_from_other_teams`	Lists the panels, gating templates, image analysis templates and protocols other teams in your organization shared with your team.	Read only
Copy a shared record `copy_record_from_other_team`	Copies a record another team shared into your project, where you can change, score or run it.	Read and write

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