What is new in Omicsboard Lab 1.5.49

Version 1.5.49 of Omicsboard Lab is out for Windows and Linux. It is mostly about making your work easier to follow, easier to correct, easier to defend and easier to keep. Most of the interface changes are already live on the web app too. Where something is desktop only, we say so.

In this post: The notebook · The plan · Reports you can defend · Your project folder · Team plans · Smaller things · More from this release

A notebook you can work in

• Code that reads like code. Cells are colour-coded with line numbers, and long lines scroll sideways instead of wrapping.
• Tidier results. Printed output sits under a small Output label, tables lose their hard grid lines, and wide tables scroll with an Expand table button. The built-in analysis cells are now written one statement per line.
• Figures that check themselves. Every figure Omi draws in the local Python notebook is measured for overlapping labels, a legend sitting on top of the data and text that is too small. If the figure is fine, you see nothing. If not, Omi is told what is wrong and fixes it.

How to edit and re-run a cell

1. Click into any finished cell and type. There is no Edit button to find. The code stays colour-coded, undo works, and Esc puts the original back.
2. Run just that cell with Ctrl+Enter or the Run button in the cell’s header (hover over the cell). It runs on the same kernel, so earlier variables are still there, and the new output replaces the old.
3. Or describe the change. Choose Ask AI in the cell’s header, type what you want and press Enter. Omi writes the revised cell as a new cell, runs it and says what changed. Your original stays above it.

On your next message Omi is quietly told which cells you changed and what they printed (up to five cells), so it carries on from your version. You cannot edit a cell while Omi is working or while the cell is still running.

A chat that follows the plan

• Chat folds by step. Once your plan is running, the conversation is grouped under each plan step. Click a step’s header to open or close it. A finished step folds Omi’s working notes into one card you can open for the detail, and anything Omi could not resolve stays visible.
• Plans name the tool. Each step says which tool does the work and where it runs, whether that is your own computer, the cloud or Galaxy, so you can approve it knowing what will happen. (Desktop.)
• Your pacing words count. Say “do it all at once” or “one step at a time” and Omi remembers it. Say “keep it simple” and it stops adding suggestions you did not ask for. (Desktop.)

Reports you can defend

Omi has always written Methods sections for you. In 1.5.49 it also checks the draft against what the analysis actually did, and leaves a trail you can verify later. These checks run in the desktop app.

• The software behind every result. The Software and versions table is read from the running notebook and from the tools themselves. A package whose import failed is left out, cloud tools show the program that really ran, and a version that cannot be found says not recorded. It is never guessed.
• Claims the analysis did not earn. Omi stops a draft that says there was no contamination or no chimeras when no screening ran, presents a quick neighbour-joining tree as the result, or cites a program that never ran.
• Things left unfinished. A skipped plan step never mentioned in the report, a notebook section whose last cell ended in an error, a data or figure file named in the text that is not in your project folder, or a drafting note such as TODO still in the text.
• Wording that overreaches. “Confirms” used when no branch of the tree has more than 70 percent support, a citation to the wrong version of a tool, the same result stated three times, and sentences that describe the report instead of the findings.
• Starting from the right literature. If your data come from a public accession, Omi looks for the paper that published it first and cites it, instead of claiming the dataset is new. You can also give Omi a reference file and use markers such as [@smith2024], which become numbered citations.
• A checksum trail. Each time a report is drafted or edited, a manifest is written next to your files, listing the report, figures and saved results with SHA-256 checksums, plus the plan steps and a fingerprint of each code cell. A run you asked Omi to do all at once also leaves a provenance file. Your code and data are not copied into either file.
• Pasted tables are kept. A table or FASTA you paste into the chat is saved in your project, so it survives a kernel restart.

Each kind of problem can stop a draft at most twice per session, so a check can never trap you. These checks catch common problems. They do not replace reading the report, a checksum only proves a file has not changed since it was written, and the interpretation in the Discussion is yours to stand behind. Check your journal’s rules on disclosing the use of AI tools.

Your work stays in your project folder

In the desktop app, each lesson is now also saved inside your project folder, in an omicsboard-record folder, in a form you can open without Omicsboard:

• A readable notebook as a web page with the chat, plan, code, outputs and figures. It contains no scripts, so it opens safely.
• A full transcript in a standard JSON file the app can load again, and a short README.

The copy refreshes while you work and when you close the app, and the app’s own copy stays the main one. To restore a lesson, open the workspace menu, choose Restore a lesson from a project folder and pick the folder. It reopens on this computer, linked to that folder, and Omi can carry on. Restoring never replaces a longer copy you already have.

Team plans for your lab or group

If several people in your lab use Omicsboard Lab, you no longer need to manage individual plans. A team plan gives everyone in an organization the same plan, billed once, managed by you.

1. Verify your email, then open Settings and Plan & usage, and choose Create an organization.
2. Give it a name and type, pick Pro or Power seats, how many (2 to 150), monthly or annual billing and your currency. The total is shown before you pay. You must not already belong to another organization.
3. Pay by card. The organization is created with you as its owner.

• Add people from the Organization card by email. Someone with a verified account joins straight away, and everyone else is linked when they verify. Owners can manage admins and roles, admins can invite and remove ordinary members, and nobody can remove themselves, so an organization always has an owner.
• Usage is shown as a percentage per member. Members’ chats and files stay private from owners and admins.
• Add seats at any time, prorated for the days left. Renew before or after the end date; seats can change at renewal, but never below the people in use.
• When a plan ends, access continues for 7 days while the owner sees a banner and can renew. After that, members fall back to their own free allowance and their work stays where it is. Nothing renews automatically.

Universities and agencies that pay by invoice, or that want a shared pool for a course or project, can write to info@genomacholdings.com or read about the Omi Institutional Grant. Paying is a real card payment, so check the total before you confirm. See the pricing section for plan details.

Smaller things

• A nudge when a long run finishes. If a job takes more than 15 seconds and the window is in the background, you get a notification. You can switch it off in Settings.
• Better chat titles. Chats get a short, meaningful title, older chats that still show your first line are retitled, and renaming a chat no longer pushes it to the top of your recent list.
• A clearer update prompt. When an update is ready, a small card appears above the message box with a Relaunch now button. Settings shows the real version number.
• A friendlier start. New accounts see a short welcome card and a nine-step tour of the screen, and the first-run questions show how many there are, with two optional ones added. You can replay the tour from the Help menu on the desktop.

More from this release

• New cloud tools. A long list of tools from AMRFinderPlus and ResFinder to Bakta, Unicycler and IQ-TREE 3, a standard chain for phylogenetic trees with a tree-drawing tool that checks its own layout, and reference databases that work without a live lookup. Read about them here.
• Use Omicsboard from your AI assistant. The new MCP Connector tab lets Claude or ChatGPT run twelve Omicsboard tools on your account. Here is how to connect it.

Get it

Download version 1.5.49 for Windows or Linux from the download section, or let your installed app update itself. The web version at app.omicsboard.com needs nothing to install.