BioManager

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BioManager replaces the pile of spreadsheets, whiteboards and paper cage cards most labs run on. You edit records the way you would in a spreadsheet, but underneath is a real database. It knows which mouse is in which cage, when a litter needs weaning, which fly vials need flipping and which antibody is about to expire — and it tells you.

It runs as a desktop app for one person, or on a lab server that everyone signs in to from a browser, including on their phone at the rack.

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🔬 What you can track

	Module	In one line
🐭	Mouse colony	Mice, cages, litters, breeders, strains, experiments and racks
🐟	Zebrafish	Lines, tanks, fish, clutches, matings and water systems
🪰	Drosophila & C. elegans	Vials and plates, crosses, and temperature-aware flip schedules
🌱	Plants and field crops	Sowings, trays or plots, harvests kept as seed lots and sown again, generations and the 3:1
🦎	Any other organism	Your own database, in your own words, with no programming
🧬	Plasmids	Sequences with an interactive map, assembly of new ones, and where each tube lives; primers, glycerol stocks and viruses beside them
🧪	Lab inventories	Samples, orders, reagents, chemicals, antibodies, viruses, primers, glycerol stocks, cell lines, or a list of your own
📅	Calendar & notebook	Experiments, to-dos and colony dates; a shared lab notebook with data sheets, protocols, paper notes and meeting notes

🐭 Mouse colony

The most complete module, built around how a mouse room actually works. Tabs across the top: Mice, Cages, Litters, Breeders, Experiments, Strains and Dropdowns. My colony, My groups, Shared and Everyone change which mice and cages you see, never what you may edit.

• Mice — a spreadsheet of every animal: ID, custom tag, strain, sex, age, status, transgenes, cage, rack, owner and notes. IDs are assigned in order and never reused; the Custom tag beside the ID is however the animal itself is marked — an ear tag number, an ear punch such as RF or LB, a tail tattoo — so you can find the mouse in your hand, and search finds it by that too. A lab that doesn't mark its mice unticks it under Columns. Strain, after it, is the mouse's background — C57BL/6J, BALB/cJ, 129S1/SvImJ… — picked from the colony's strain choices (the Dropdowns tab, which starts with the common ones) or typed. A mouse is alive until it has a date of death. The dot before its ID shows its age at a glance: blue under 8 weeks, green from 8 to 30 weeks, red past 30 weeks, and grey once it is not alive.
• Cages — every cage with its Card ID (the number on the animal facility's own cage card, if it has one), rack position, purpose, the mice inside (with the sex breakdown), litter born and the P21 weaning date side by side, then its genotype and owner. Type over a cage's number to renumber it; its mice go with it. A cage's mice show the transgene columns the Mice tab shows. A cage's purpose is Breeding (a mating cage, the only one with Litter born, Genotyping and Wean), Breeder (the lab's breeding stock, shared with the lab; each person keeps part of it) or Experiment, and an admin can add the lab's own under Configure → Cage purposes. Above the cages, All, Active (cages with living mice) and a button per purpose show just those cages; a purpose's button lists only its cages with living mice, and All still shows the past ones. Each cage shows its mice beneath it, to edit right there and wean (Close all folds them to one row each), or switch to Cards: a card per cage with its mice and its actions, as on a rack. A position in a rack can hold more than one cage (a new cage is often set up there before the old one is ended): the Rack grid shows the one put there last and marks the position ! while two or more there have living mice; hover over or tap the ! to list and open them all. Its Unplaced list holds the cages with living mice that have no position yet; empty cages stay out of it (the table still lists them). Changing a rack's rows, columns or position names asks first what happens to the cages in it, listing each: Keep each position name (F7 stays F7, in the cell called that now) or Keep each in the same cell (its name changes); one the new layout has no place for stays in the rack, unplaced. Fish racks, fly and worm racks and boxes ask the same.

🐟 Zebrafish

Lines with their ZFIN names and founders, tanks, individual fish, clutches, water systems and a sac log. Set up a mating records which tanks went in and when they go back, and they stay on Home until someone marks them Returned; New clutch records each fertilisation against its cross. Log reading keeps each system's temperature, pH, conductivity and salinity, with a chart, and can raise an alarm. A tank can hold a group with a headcount, or resolve into named individuals. A fish row's dot is blue under 3 months post fertilisation, green to 18 months and red after. The Experiments tab, beside Tanks and Fish, works as the mouse colony's does, with fish in mind: start with a tank's fish rows, or a clutch's larvae, record drug in the water, microinjection, a heat shock or an injury, and follow survival (how many of those at the start are still alive), standard length or a phenotype.

🪰 Drosophila and C. elegans

Vial (fly) and plate (worm) databases: vials in racks and plates in boxes, inside incubators, each incubator at its own temperature.

• Label each vial with its genotype and purpose: stock, experiment, cross or progeny.
• Set up crosses, Collect eggs into a new vial (worms: Pick progeny onto a new plate), and see when the progeny will be adults.
• Flip / chunk schedules that follow temperature — flip every 14 days at 25 °C, every 28 at 18 °C, set in the database's Settings → Temperatures and timing — and a rack moved to another incubator changes its schedule by itself. Schedule shows what is overdue, due today and coming up, and each fly or worm database has its own card on Home.
• Each rack's grid says when it was last flipped and when the next is due (red when overdue), with a Flipped today button beside Edit.
• A vial's or plate's dot is blue while its progeny are still developing, green once they are adults, and red once it is older than its rack's flip or chunk interval.
• Worms: New frozen lot records a freeze, to thaw onto a plate when a line is lost.
• An Experiments tab for vials or plates (a rack's at once), with the manipulations flies and worms get: drug in the food or on the plate, RNAi feeding, a temperature shift, starvation, infection, flipping to fresh food. They have no body weight, so the readout is survival (how many of those at the start are alive), or eclosion and climbing for flies, brood size and paralysis for worms.

🌱 Plants and field crops

Add database → Plants (pots and trays in growth rooms or a greenhouse) or Field crops (plots in a field, raised first in a nursery and transplanted) makes a database that speaks of plants: it is Sown and Harvested, not born and dead, and has no sex.

• Sowings — each with its date, the seed lot it came from, its generation (T2, F3) and its stage (seedling, transplanted, flowering…, or the nursery for a field crop). The Schedule counts days after sowing: out of the cold, count germination, transplant, harvest.
• Seeds — every seed lot: its line and generation, where it was harvested from, how much is left (mg, g, seeds or tubes), where it is kept, its germination, and its descent back through each sowing and harvest to the first lot. The wheat button on a plant, a sowing or a cross harvests its seed into a new lot a generation on (seed from a cross is F1) and can mark the plants harvested; Sow on a lot starts a sowing from it and takes the seed off what is left. Labels prints them for tubes or packets.
• The selection plate — type a T2 lot's resistant and sensitive seedlings and the sheet says whether they fit 3:1 (one insertion), 15:1 (two), or all resistant (homozygous), by χ².
• Lines keep their background, source and stock number, selection marker, whether they are transgenic and under which biosafety permit, and the construct: a plasmid from the Plasmids database, linked.
• Places are growth rooms, growth chambers, greenhouses, nurseries or fields; a field is a grid of plots, as a rack is of cages. Readings log temperature, humidity, light and day length.
• A plant's dot is blue while it is a seedling (under 14 days), green, then red past 70; every number and word here can be changed in Configure.

🦎 Any other organism

Choose Add database in the sidebar, start from a mouse-like, zebrafish-like, plant-like or blank organism, and describe it:

• The words it uses — cage, tank, vial or plate; strain, line or stock; litter, clutch or progeny. The interface then speaks your language. Age can be counted in days, weeks, days post-fertilisation, generations or passages.
• How it is counted — individual animals, groups with a headcount, or both.
• What it needs, from a checklist — crosses, cohorts, a nursery stage, genotyping, environment logs, cryo inventory, seed lots, census and more.
• Its own words for its dates (Hatched, Sown), its stages and the kinds of place it keeps them in, under Configure; leave Sexes empty and the Sex column goes. Young until and Old after colour the dot before an ID by age.
• Schedules like "wean at P21", which can vary with rearing temperature. Each rule counts from its own last Done (feeding doesn't restart the split's clock), and Done can be dated to the day it was really done.
• Your own columns — text, numbers, dates, dropdowns, people, links or a plasmid, edited in the sheet like the others and set on many rows at once.
• An Experiments tab, the same as the mouse colony's, on your animals, groups or cohorts (a housing's at once), with body weight, length, survival or your own readout.
• Who it is for — just you (a personal database only you and admins see), or the whole lab.

[!TIP] Xenopus, axolotls, cell lines, yeast strains — anything you keep in containers and breed or passage fits here. No code and no migration.

Only what your lab keeps, in the order you work. No database is there by default, the mouse colony, zebrafish and plasmids included: the lab adds what it uses (from the setup survey, or Add database → Ready-made databases), and an admin can switch one off in Settings → Databases without deleting anything; its records come back when it is switched on. An admin drags the databases into the lab's order right in the sidebar (or All databases → Order in the sidebar), the same for everyone. All databases groups them into Animals and Molecular & supplies, and every database has the same two buttons beside its name: Configure (for whoever may change it) and All databases. Icons are picked from a grid of the icons themselves.

🧬 Plasmids

Upload a GenBank, FASTA or SnapGene file and BioManager keeps the sequence and its features, with an interactive map you can edit. Plasmid boxes sit on the same rack grid as everything else, so every tube has an address. Each tube keeps its miniprep's concentration (ng/µL) and 260/280, and a plasmid can be Lab common: anyone can edit it (or, shared with a project group, its members), while its owner still decides whose it is. A plasmid's page lists the notebook pages that @plasmid it, and its address is its number (plasmid #12 is /plasmid/12). Show them as a Table, by storage Boxes, or as a List. In the sheet, Sequence beside a plasmid's number opens its sequence and map (Add sequence when it has none yet). Download gives it as GenBank or FASTA, and Versions keeps every earlier sequence to restore. Made from records its backbone, insert or template (in the lab or from Addgene) and how it was made; its page shows what it was made from and what was made from it, with a family tree. Assemble a plasmid builds the next one from the ones you have: fill a tray with fragments — a whole plasmid, one feature, a region, or a piece an enzyme leaves — and put them together by digest and ligation, by Gibson / NEBuilder HiFi, or by Golden Gate. Every junction shows its own bases, and one line says what is wrong and which end it is ("Fragment 2's 3′ end has no overlap with fragment 3") before you make anything. The product arrives as an ordinary plasmid, with every fragment's features at their new places, each fragment marked on its map, Made from filled in for all of them, and — for a Gibson — the primers it needs designed, costed by melting temperature and waiting in the Primers database to order. Primers, glycerol stocks and viruses each name the plasmid they came from, so they are tabs of one area rather than four entries in the sidebar: Molecular biology, called just Plasmids while the lab has none of them. The Feature library keeps the lab's elements (promoters, ITRs, LTRs, WPRE, resistance genes) by sequence, from any well-annotated map, and Detect features marks them on another plasmid; a lab that installs pLannotate on its server also gets Annotate with pLannotate, which finds elements by alignment rather than exact matching. Nothing is built into the library: its elements come from your own files (Add to library above a map, or Read elements from files), and an admin can , about 1,900 elements from widely used plasmids, downloaded when asked for. on its Storage tab keeps the sequencing reads, gel photos and datasheets that belong with it, and they come along in Export my data. , below the map, checks Sanger reads of a miniprep or clone against it: choose the chromatograms (or FASTA, or paste the bases) and each read is trimmed of its poor ends, placed on the map on either strand (across the origin too), and compared base by base. You get a line for the clone ("Matches the map across 425–1,359, covering EGFP", or "1 difference from the map: C→A at 740 in EGFP (A14D)"), where the reads lie over the map, and every mismatch, insertion and deletion with the read's quality there, the features it falls in and what it does to a coding sequence's amino acid; one at low quality is marked as a likely sequencing error. From an , each difference shows its stretch of trace, and a read with second peaks under many bases is said to look like a mix of two clones (and where they part, when an insertion or deletion splits them). files them under , each noted with what it showed, to check again later. An assistant can do the same with , from reads uploaded as captures. A primer drawn on the map is kept in the Primers database, linked to the plasmid; the page lists where each binds, and or gives the ticked ones to your oligo supplier. Before ordering another, looks through every primer the lab has saved, whichever plasmid it was made for, and lists the ones that bind this sequence — exact matches, and those matching at the 3′ end with a 5′ tail — and draws them on the map to look at, without saving them into it.

Every database takes columns of your own — Configure → Your own columns, on the mouse colony, zebrafish and plasmids as on the others: a weight, a score, a date, a choice from your own list. They show in the sheet and in each record, and come along in Export my data. Taking a column away hides it without losing what your records hold in it.

🧪 Lab inventories

Every inventory runs on the same engine, starting from a preset you can change:

Preset	Tracks
🧫 Samples	harvested tissue and material, linked to the animal it came from (type its ID in Source, or set a whole harvest at once), with that mouse's Custom tag beside it and its Genotype from the colony, and its sex, age, genotype, status, owner and cage on hovering the arrow that opens it; a tab for each type (tissue, blood, DNA, RNA… and any you add with +), each with its own columns: a tissue's Tissue, Fixation and Orientation, a DNA's or RNA's concentration, unit, 260/280, 260/230 and volume as numbers; stored at RT / 4 °C / −20 °C / −80 °C / LN₂ in a box position
🛒 Orders	a board from requested to ordered to received, with vendor, catalogue number, price and grant account
⚗️ Reagents	quantity (with a Low at level that marks a bottle low as it runs down), concentration, CAS number, hazards (several per bottle), supplier and lot, and expiry dates with warnings
🧂 Chemicals	your lab's chemical list: name, abbreviation, CAS number, molecular weight, purity and density, with lot, expiry and where each bottle is, and its hazards, several at once, including the controlled classes a safety office asks about (drug and explosive precursors, highly toxic); a Formulation in the notebook picks from it and works out the moles, and Utilities' calculators know each molecular weight
🔬 Antibodies	host, clonality, clone, conjugate, reactivity, applications, dilution, RRID and where each vial is stored
🦠 Viruses	AAV, lentivirus, rabies and other vectors: serotype, promoter, payload, titer, biosafety level, the date made, and the plasmid each was made from — which opens that plasmid, or its sequence and map to read, and whose page lists every virus made from it
🧬 Primers & oligos	sequence, direction, target and pair, with length, GC % and Tm worked out from the sequence; Add primer pair makes the forward and reverse at once, linked and side by side in a box; a primer drawn on a plasmid's map lands here with the plasmid named, Find saved primers on a plasmid lists the ones here that already bind it, and Copy for ordering / Export for ordering hand the ticked ones to your supplier

Each inventory can keep your own stock apart from lab common stock, and statuses and categories can be renamed without losing items. Renaming a database moves it to its new name's address; the old one keeps working, so printed labels, bookmarks and @mentions still find it. Every database has a name of its own (one another database has is refused), so @ and a name in a notebook page always means one database.

• A tab for each type — Samples opens on All, with a tab beside it for each type: Tissue shows only tissue, with the columns a tissue has, and its boxes; DNA shows its concentrations and purities. A new sample made from a tab is of that type, and the dialog asks only for the columns used for the type chosen. + at the end adds a type; which columns each type uses is Used for in Configure, and any inventory can turn on A tab for each type.
• Split notes — a sheet brought in from somewhere else often left everything in the notes ("Tissue: Lung; Fixation: 4% PFA; control 2w"). Tick the rows and Split notes: each "Column: value" goes into the column of that name, the rest stays in the notes, and Batch history can undo it.
• Filter orders by status — one tap shows only what is requested, ordered, received or cancelled.
• Expired is red — a reagent, chemical, antibody or virus past its expiry date has a red dot, number, name and date; Expired and Expiring soon show only those.
• Low stock says so itself — give a reagent, chemical, antibody, virus or primer a Low at level, in the unit of its quantity. When the quantity falls to it the status turns low (at 0, empty) and its owner is told; a reagent, chemical, antibody or virus is then listed on Home's Expiring & low stock with what is left. Topped up above it, it is in stock again. A quantity in words ("half a bottle") is left as it is, and so is a status set by hand.
• Kept in ampoules, used in mL — an item counted in ampoules, vials, tubes or bottles can have a Pack size, what one of them holds (10 mL), in the dialog and as a column you can show in the sheet. An AI assistant told "2 mL used" then takes 0.2 of an ampoule off its quantity; without one it says what is missing rather than guess.
• Nothing half-filled — an order can't be placed without its item, vendor, catalogue number and quantity. Configure chooses what any inventory requires.
• Type it once — every column suggests what the lab has typed before; pick an earlier item or catalogue number and the vendor, price and grant fill themselves in.
• Order again — one click on a reagent, chemical, antibody or virus starts a new order with its details, and the quantity, price and grant of the last time. A record that is already on order shows On order, and Order again says which order is open and who asked for it.

📅 Calendar and notebook

• Calendar — experiments and to-dos, with colony dates (weanings, genotyping, sac reminders), fly and worm flips, organism schedules and reagent expiry filled in for you. Shows your Google Calendar and any iCal subscription alongside, read-only, under Connected calendars.
  • Who sees it: an event or to-do is yours alone, the lab's or one of your project groups'. Your own is seen by nobody else, admins included. A shared event is everyone's to see, its owner's and the admins' to change; a shared to-do anyone it is for can tick off.
  • Repeating events: every so many days, weeks or months (every 2 weeks, say), or every month on the same weekday ("the first Monday"), until a date. One date can be taken out (Delete this one) or changed on its own (Change this one only).
  • Protocol timelines: write the steps once in days from day 0 (tamoxifen days 0–4, implant day 14, perfuse day 42), start them for an experiment or cohort, and every step lands on the calendar. Move day 0 and they all move.
  • Equipment booking: time on the confocal or a rig; double bookings are refused, saying who has it. A booking can repeat every day, weekday or week until a date (if one repeat clashes, none is made), and Duplicate books the same instrument and times on another day. Instruments are added, renamed and removed under Manage.
  • Time away: leave and conferences, with what falls due while you are away and who covers it (they are told).
  • On your phone: a private link that Apple, Google or Outlook Calendar subscribes to, with just your things or the whole lab; it updates about every hour, and Make a new link stops the old one. Google fetches the link from the internet, so it needs a server open to the internet.
  • Mac Calendar, in the desktop app on a Mac, with no server needed: BioManager keeps a calendar called BioManager up to date in the Mac's own Calendar app, which takes it on to iCloud, Google or Outlook, and so to your phone. Choose just your things or the whole lab, and where it goes. For Google, first make a calendar called BioManager in Google Calendar on the web, because a Mac can't add one to a Google account. It updates while the app is open: every 15 minutes, and soon after a change. The calendar is BioManager's alone, and Stop takes it out again.
• Lab notebook — pages in topics, written like a document and saved as Markdown. Topics are folders, and a topic can hold topics of its own, as deep as you like: a page stays in the one it was made or moved to, whatever its kind. The notebook has one sidebar of its own (BioManager's folds to its icons there): at its top your notebook's name opens , makes a in the topic you are in, and narrows the list as you type (Enter searches inside every page); and the libraries stay at its foot. In the sidebar, beside names a new one, a topic's own starts a page in it, and makes a , changes its (one of BioManager's icons, any emoji from your computer's emoji picker, or an SVG drawing of your own), moves it () or deletes it (the topics inside it stay, one level up). Drag to tidy up: a page onto a topic moves it there, between two pages puts it there, and a topic onto another goes inside it (or above or below, near its edge). A topic's name opens its own page: the topics inside it as tiles, then its pages as cards or a list, by , or . The star on a page or a card keeps it in at the top of the sidebar (once there is one), in your order. The notebook opens on : your favourites, what was edited lately and your topics. holds the pages in no topic yet; protocols, papers and talks, and a meeting series' notes are in , and instead. The sidebar hides (its button, or Ctrl+\ / ⌘) to give the page the window. asks for a title, the topic, the kind of page and what to start from (a built-in starter or one of your templates). A page's kind sits above its title, saying what it adds; click it to change the kind, which never moves the page. A long title wraps onto more lines, set well above the page's headings as in Notion, and puts a picture across the top. Above the page its place reads like a path (the topics its topic sits in, then its topic); click the topic to move it. A page links to mice, plasmids, orders and any inventory record (, ): type and a name (written as it is, or ), a catalogue number or lot, a database's name ( offers Antibodies and lists its records) or a colleague's name, for ; the chip shows the record's name after its number, and its popover shows its lot and place. The record's dialog lists the pages that link it (), so the record and the notes point at each other. A colleague's is shown in their colour, and hovering it shows who they are: name, what they do, admin, member or guest, email, project groups and since when. Type on a new line for everything below (Chinese words find things too, ).

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✨ Features across the app

📥 Coming from Excel

Every database has Import from Excel, under ••• at the end of the toolbar above its sheet: mice, fish, plasmids, fly and worm vials, any organism database and every inventory. Upload the workbook (.xlsx, any sheet), CSV or TSV you kept your records in, as it is (up to 15 MB and 5,000 rows):

• Columns are matched by meaning, not just by name. Position, Slot and Well are the position; DOB and Born the date of birth; Supplier the vendor; Cat. No. the catalogue number. Where a name could mean two things the values decide: a Location of A1, B2… is a position in a box, one of Freezer 2 is a location note. Chinese headers count too (性别, 出生日期, 笼号, 质粒名称), in a CSV saved by Excel on a Chinese Windows as well. Each match says why it was made, and you can change any of them.
• The database adjusts to your sheet. A column BioManager doesn't have becomes a new column (text, number or date) in inventories and organism databases, if you may configure them, and a mouse sheet's columns are matched to the colony's own columns too. Anything else goes into each record's notes as Header: value (or Leave out skips it), so nothing is lost.
• Must-have columns are filled in. If your sheet has no owner, say who every row belongs to (you, by default); for plasmids and stock, whether every row is Personal or Lab common (or a Lab common column says so row by row).
• Values are tidied. Excel dates in any style (day or month first, decided per column and otherwise by the lab's date style in Settings → General, 12-May-26, or a date number; a future date of birth is left blank and kept in the notes), Male/m/♂/公 → M, your lab's own statuses, people by name, a plasmid's 152.6 ng/µl as its concentration. A cell merged down over several rows (a Cage # typed once for its mice) counts for each; typed once with blank cells below instead, a cage, rack, box or tank column offers Its blank cells take the value above them, ticked (untick it if a blank means none). Cages the import makes belong to their mice's owner.
• You see a preview first. It runs through the same checks as the database's own dialogs and lists every row that would be skipped and why, by its row number in Excel. A Total line under the records is left out, and a mouse whose ID is taken (by the colony or an earlier row) gets the next free one, with the preview saying so. The import itself is one batch, so Settings → History can undo it.
• Then renumber, if you like. An inventory record's # follows the order its rows came in. → (for the inventory's creator or an admin) gives every record the number in its name ( becomes #12, when every name has one, none twice and none missing; it names the records in the way) or numbers them in the order of a column (B2 before B10). It shows each # now and new first; notebook links () and orders put into stock follow, printed labels keep the old # (their QR code still opens the record), and it is one batch to undo.

📱 Cage cards that open on your phone

Print correctly sized cards and labels: Cage cards on the Cages tab, Tank labels for zebrafish, Labels on a fly or worm database, and Labels on ticked samples, reagents or any inventory's rows. Scan the QR code with any phone camera at the rack and that cage opens, ready to edit — nobody walks back to a computer to type an ID. On a phone every sheet row becomes a card with its columns under their names, and rack grids get a Move button: tap a cage, then where it goes.

• On a phone: Android has its own app (BioManager-Android.apk from the download page; Scan reads cage cards). On an iPhone or iPad, open the lab server in Safari and Share → Add to Home Screen: it opens full screen like an app, and the camera scans the cards. Phones reach a lab server, or a desktop that shares its lab on the network. A bar at the bottom of the screen holds Home, Calendar, Databases, Notebook and Scan, with Search beside it.

• Label printers: Print on chooses a sheet of cards for any printer, or a label printer's roll — Brother QL (62 × 29, 90 × 29, 100 × 62 mm), Zebra (2 × 1, 3 × 1, 4 × 2, 4 × 2.5 in) or cryo-tube labels — and prints one label a page, typed to fit. Each person's choice is remembered.

• What each label says: for tubes, On each label chooses the fields (box, position, lot, a column such as concentration, the day printed…), remembered for each database, and Two lines for long text wraps a cryo label's name and place instead of cutting them.

• Zebra: Download for Zebra (.zpl) gives the labels in the printer's own language. Or an admin adds the Zebra's address once, under Send labels straight to a Zebra on the network, and Send to Zebra prints them straight away.

🌗 At home on a Mac, and in the dark

The interface follows Apple's Liquid Glass design: the sidebar, the row of tabs and each page's buttons float as frosted glass over the page, which scrolls beneath them, while the records themselves sit on solid ground so they stay easy to read. On a Mac the desktop app has no title bar; its close, minimise and zoom buttons sit at the top of the sidebar, followed, as in Safari, by buttons to hide the sidebar, search everything, and go back and forward. Hidden, the sidebar narrows to a column of its places, each icon with its name under it. There is a full dark mode, following the system's setting (in the desktop app, View → Appearance chooses Light or Dark), and Reduce Transparency, Increase Contrast and Reduce Motion are honoured. It works in any modern browser on Windows and Linux too.

Text is set in Inter, which tells I, l and 1 apart in IDs and genotypes and looks the same on every computer, with each system's own Chinese font. Settings → Appearance & language → Font switches to the computer's font, and Text size makes everything smaller or larger in the Mac app.

Settings is laid out like the Mac's System Settings: a list of panes on the left (You: Profile, Sign-in & security, Appearance & language, Notifications, AI assistant & tokens, Your data; Lab: Statistics, General, Databases, People & access, Devices & copies, History) and the chosen one beside it, its settings in grouped rows with a short line on what each does. A change is saved as it is made, and the search box at the top finds a setting by name. Your Short name under Profile (up to 5 letters, THX) is what your round badge says, at the top right and on your records; without one it shows your initials. The lab's panes hold its setup and its admin pages: everyone sees them, admins change them. Statistics counts the lab's mice, fish tanks and fly and worm vials, by person, and shows how full each rack and box is.

Each person can pick their own app icon in Settings → Appearance & language: a double helix, mouse, zebrafish, C. elegans, Drosophila, cryobox, microtube or petri dish, in one of six macaron colours. The browser tab and sidebar show it, and the app's accent colour follows it.

🌏 English or 中文

BioManager is in English and Simplified Chinese. It follows the language a person's computer or browser asks for first (the desktop app, the computer's); each person can choose for themselves in Settings → Appearance & language, which changes as soon as they pick, or with the 中文 / English switch on the sign-in page, which stays their choice once they sign in. Every page is in both: each database, the calendar, the notebook and experiments, Settings and the lab's panes in it, and the messages and notifications, which reach each person in their own language. Names, notes and everything people type stay as written, and so do exports, labels and the API. The website has a Chinese version too, at biomanager.org/zh.

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🚀 Ways to run it

flowchart TB
    subgraph one["💻 Desktop app"]
        direction LR
        A[You] --> B[BioManager.app] --> C[(SQLite on<br>your computer)]
    end
    subgraph lab["🏫 Lab server"]
        direction LR
        D[Lab members<br>laptops & phones] -- HTTPS --> E[BioManager] --> F[(PostgreSQL)]
        F -. nightly, tested .-> G[Backups]
    end

	💻 Desktop app	🏫 Lab server	🛠️ From source
For	one person, one computer	a whole lab, from any browser	developers
Database	SQLite, on your computer	PostgreSQL	SQLite (or PostgreSQL)
Setup	download and open	the desktop app sets it up for you (or Docker by hand)	Python 3.11+ and Node
Backups	dbtool.py backup	automatic, nightly, test-restored weekly, optional off-site copy	dbtool.py backup
Phones & QR codes	— only your computer, unless it shares its lab on the network	✅	on your local network

[!NOTE] Start on the desktop and move to a server later: Set up a lab server in the desktop app can bring this computer's records along (by hand, scripts/migrate-to-postgres.py carries an existing database across).

🔁 One lab, many devices

One device holds the lab's master copy; every other one works on it through its address, so nothing is ever merged and nothing written in two places is lost. Settings → Devices & copies → Devices says which device it is and lists every computer linked to the lab:

• A lab server is the master copy unless an admin hands it on.
• A desktop joins the lab as one of your devices (Open your lab, or Open the lab in this window): you sign in as you do at the lab (or approve a code on a device already signed in), and its window works on the lab through the app, never the server's page itself. It keeps a daily copy, locked with the lab's key and its own. Go → This Computer's BioManager and Go → Your Lab's BioManager switch between the two.
• A desktop can share its own lab on the network (Share this lab on the network, admins): it becomes the master for every device on the same network (Wi-Fi or cable), which opens its address. The computer must stay on, and the connection isn't encrypted, so only on a network you trust.
• An admin can hand the master copy to a linked desktop (Make it the master, for a computer with an admin's key, open, on the same version). It takes a last copy, keeps its own data as a backup, and shares the lab on its network; the old master turns read only and sends everyone there. Give the master copy back returns it, with everything changed meanwhile. Sign-ins to other services (Google Calendar) are not carried along and are connected again.

Every computer, phone and browser you are signed in on is one of Your devices (Settings → Devices & copies): rename one, or Sign out one (a lost phone) without changing your password. Admins see everyone's.

📴 Working offline in the facility

Animal facilities often have no signal. The Android app and the desktop app keep a copy of what you need there (the colony's racks, cages, mice, litters and recent weights, your to-dos for two weeks, vials and tanks, as you may see them), refreshed when they open, when the network comes back and every 15 minutes; Get ready for the facility (hold the Scan button) takes a fresh one. When the server can't be reached, the app shows offline screens instead of an error: find a cage by its ID or card, or scan it, and Record a weight, Died, Move, Note, Litter born, Genotyping, Wean, tick a to-do, flip or discard a vial. A Breeding cage lists each litter not yet weaned, and Litter born, Genotyping and Wean ask which, as the pages do. Each shows at once, marked waiting. Back in signal the changes reach the lab in the order you made them, through the pages' own rules, as you. One that clashes with a change made meanwhile (the same field, set to something else) waits under Needs your decision (Keep mine, Keep theirs, Edit); a different field is kept along with yours; one the lab refuses is listed with the reason.

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🏁 Getting started

💻 Desktop app

1. Download BioManager for your system from the BioManager website, or build it yourself (below).
2. macOS: open the download and drag BioManager into Applications. The first time, macOS won't open it: choose Done, then System Settings → Privacy & Security → Open Anyway (before macOS 15, right-clicking the app and choosing Open is enough). Windows: extract the zip, open the BioManager folder and run BioManager.exe; at the warning choose More info → Run anyway. Linux: mark BioManager-Linux.AppImage executable and open it. The apps aren't signed by Apple or Microsoft, so the system asks once per version.
3. It asks whether your lab already uses BioManager. Yes, open my lab takes the lab's address, then your sign-in, and joins the lab as one of your devices; nothing is made on the computer. No, start a new lab names the new lab, asks where it lives, and makes your account its admin; then answer the short setup survey: tick what your lab keeps, and BioManager creates just those databases, with racks and incubators to match, and shows the address people join at. Home then shows a Getting started list of first steps. Before moving a real colony in, the guide's Try it first walks through a practice rack, a litter and its weaning date, then throws it away.

On a Mac the app has a full menu bar: File (New Tab ⌘T, Close Tab ⌘W, Export This Sheet ⇧⌘E, Print ⌘P), Edit (the usual editing commands and Search BioManager ⌘K), View (Reload ⌘R, zoom, Light or Dark whatever the system uses, Full Screen), Go (Back ⌘[, Forward ⌘], Home ⇧⌘H, next and previous tab ⇧⌘] ⇧⌘[, and everything in your sidebar, the databases on ⌘1 to ⌘9), Window and Help (the user guide, keyboard shortcuts, what's new, report a problem). Settings… is ⌘,. On Windows and Linux the same destinations are in File, Go and Help.

Check for Updates… (in the BioManager menu, or Help on Windows and Linux) asks GitHub for the latest release and, if it is newer, shows what's new. Install and Restart downloads it, checks it against the checksum GitHub publishes, and swaps it in as the app quits (the old one is kept until the new one opens); where it can't (the Linux .tar.gz, a folder it can't write to), it opens the download in your browser. The app also checks by itself, at most once a day; turn that off with Check for Updates Automatically. The check sends nothing but the app's version.

A lab server looks for a new version once a day and tells its admins (a notification, and Settings → Version, with what's new and a link to the release notes). Update now there takes a backup, downloads the new version, checks it against the checksum GitHub publishes, installs it and restarts the server; BioManager is away for a minute or two and the page comes back on the new version. It needs the server's helpers installed once (sudo host/install.sh, which every set-up route runs); without them the pane says so, and the runbook's "Updating the app" does the same by hand. The check sends only the server's version; turn it off there, or for the server with BIOMANAGER_UPDATE_CHECK=0. The phone apps open the server, so they are always on its version.

After an update (the desktop app's, or the lab server's), the first page each person opens shows a short What's new: what is new, what works differently and what was fixed, with a link to the full release notes. Got it closes it for good; Help → What's new opens it again.

The window keeps you signed in and keeps your tabs from one launch to the next, as a browser does.

On Windows the window is Microsoft Edge WebView2, which Windows 11 has. A Windows 10 PC without it gets an offer to download it from Microsoft, and BioManager opens in the web browser meanwhile (leave its message open while you use it); once it is installed, BioManager opens in its own window again.

Your data lives outside the app, so updating or reinstalling never touches it:

System	Data folder
macOS	~/Library/Application Support/Biomanager/
Windows	%APPDATA%\Biomanager\
Linux	~/.local/share/Biomanager/

./scripts/build-desktop.sh
open dist/BioManager.app

This produces dist/BioManager.app on macOS, or dist/BioManager/ on Windows and Linux.

🏫 Lab server

The easy way: let the desktop app do it. In the desktop app, choose Set up a lab server (when you start a new lab, or in Settings → Devices & copies) and say where it should run:

• a cloud server reached privately over Tailscale (recommended; Oracle's free tier is enough), or one with the lab's own web address;
• a university or department server;
• a Linux computer in the lab (a NAS with Docker, such as one running fnOS, will do), or this computer if it has Docker.

It signs in over SSH with your key, or with the account's password if you have no key (as on a NAS: under SSH key, choose No key: sign in with a password), and asks for a password for sudo too when the account needs one; passwords are used for that one run and never saved. It installs Docker (and Tailscale) if needed, downloads the release's server bundle, writes its settings with a fresh database password, can bring the desktop app's records along, starts it (on ports 80 and 443, or others it finds free when the machine already uses those, as a NAS's own web pages often do), sets up alerts and backups, and checks that it answers. Every step and every command is shown before and while it runs; at the end you get the address and the setup code for the admin account.

A lab already in the desktop app goes to a new server whole: in the desktop app, Settings → Devices → Move this lab to a server, with the server's address and setup code. Records, accounts and uploaded files go there; the desktop then opens the server and keeps a daily copy, and its own lab stays as it was, read only (Use this computer's own lab again brings it back). A server it can't reach takes the lab as a file instead: Save the whole lab on the desktop, then Bring a lab from the desktop app on the server's This server has no lab yet page. To start a server's lab over, deploy/RUNBOOK.md has a script that sets the lab aside (and puts it back).

By hand: the supported setup is the Docker stack in deploy/: HTTPS, PostgreSQL, and a backup service that dumps the database every night, checks each dump and test-restores one every week.

git clone <this repository> biomanager && cd biomanager/deploy
cp .env.example .env && chmod 600 .env     # set DOMAIN, POSTGRES_PASSWORD, TZ
host/ports.sh                              # 80 and 443, or free ones if those are taken
docker compose up -d --build
docker compose logs app | grep "setup code"

Open https://<your domain>/register (with the port, such as :4443, if host/ports.sh chose other ones) and create the first account with the setup code from the log. That account is the admin; signing in, it answers four questions about the lab, and BioManager sets itself up to match.

[!IMPORTANT] Keep the server off the open internet: on the campus network, a VPN, or a private network such as Tailscale — deploy/README.md walks through it. deploy/RUNBOOK.md covers what to do when something goes wrong.

python3 -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt
(cd frontend && npm install && npm run build:css)
PORT=5055 python run.py

Open http://127.0.0.1:5055 (on macOS, AirPlay holds port 5000). The first account needs the setup code printed in the terminal.

Want something to click around in? python scripts/demo-data.py /tmp/biomanager-demo builds a made-up lab — the one in these screenshots — and BIOMANAGER_DATA_DIR=/tmp/biomanager-demo python run.py opens it.

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📆 A first week with BioManager

A walk-through for a mouse colony. The other modules work the same way.

Open the breeding cage, choose Litter born and confirm the date of birth (today unless you change it). The weaning and genotyping dates appear on Home and the calendar when they come due. At weaning, add the pups with Add many and move them to their new cages. If the cage's last litter isn't weaned yet, say whether this is Another litter (both are kept, each with its own dates) or Correct the date.

Tick the mice on Mice (shift-click selects a range). In the bar that rises from the bottom, choose Add to experiment and name the treatment group. On the experiment, list each injection, challenge or weighing day under Regimen, then Record manipulation as each is done: a dose per body weight is worked out from each animal's latest weight. Add to notebook puts all of it in a notebook page.

Open Settings → History and undo the bulk action. For a single edit, the change history shows what the value used to be.

Choose Add database, pick a preset (Drosophila, C. elegans, zebrafish, mouse, plants, field crops) or start blank, name things your way and choose what it needs to track.

Keys	Does
⌘/Ctrl + K	Search everything
⌘/Ctrl + B	Show or hide the sidebar
Alt + 1…9	Switch to tab 1 to 9
Alt + ← / →	Previous / next tab
Alt + W	Close the current tab
Middle-click a tab	Close it
Shift-click a row	Select a range
⌘/Ctrl + D	Fill down, in the mice's Add many preview
Esc	Close a menu or dialog

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👥 Accounts, permissions and privacy

• The first page is the lab's sign-in: its name and what it keeps on one side, the form on the other. Remember me on this computer offers the account by name next time. Ask to join sends a new person's request to every admin, and their page changes the moment one approves; a visitor enters a guest code, or, without one, asks the lab's admins for one (a notification to each of them, as Forgot your password? is). Before there is any account, it starts a lab instead: on a server it says it has no lab yet; the desktop app first asks whether the lab already has a BioManager to open.

• The first account is the admin. On a server it needs the setup code, so nobody else on the network can claim it first.

• New sign-ups wait for an admin's approval, under Waiting to join in Settings → People & access; Approve lets them in.

• A lab nobody can sign in to on the desktop app (the admin's password lost, or someone else made the first account): Start a new lab on the sign-in page (or Settings → Lab) sets it aside in the data folder under old-labs, deleting nothing, and the next start begins an empty lab whose first account is the admin. Bring back a lab set aside lists them and brings one back, setting the present lab aside in its place, so either step can be undone.

• You edit what you own. Your mice, cages and records are yours. Shared cages and anything marked lab common belong to the whole lab. A Breeder cage starts out shared; any other cage starts personal. Only a cage's owner or an admin shares it, makes it personal or gives it away. The same goes for everything with an owner, in every database: editing a shared breeding tank, a lab stock vial or a lab-common plasmid doesn't make it yours to give away (animal care may, for the animals, cages, tanks and vials they look after), and a new owner must be someone in the lab, picked from the list. Admins can change anything, and when a record isn't yours, BioManager says whose it is. Racks & boxes, in Settings → Statistics, says who may change each rack, box and incubator.

• Project groups. Some of the lab working on one project can be a group (Settings → People & access → Project groups): an admin makes it, and an admin or the group's leads add and remove people; someone can be in several groups. Each person in a group is a Lead, a Member or , and the group's switches say what its members may do: edit what is shared with it, add and change records in its databases, edit each other's records there, edit its notebook pages, tick off its to-dos, and share their own things with it. They start as groups always worked. Wherever something can be shared with the lab, it can be shared with one of your groups instead: a cage, a breeding tank or a lab stock vial is then its members' to edit (as the group allows), as is a plasmid or reagent shared with it (everyone still sees them). A database made for a group is seen only by its members (and admins), a group's to-dos are on their calendars for any of them to tick off, and a notebook page or template can be shared with a group. The colony's view shows the mice and cages of everyone in your groups. Deleting a group makes what was shared with it its owner's own again (a breeding tank or stock vial the lab's).

💾 Your data and backups

[!WARNING] Don't keep the database in a cloud-synced folder (OneDrive, Dropbox, Google Drive, iCloud Drive). Syncing corrupts SQLite files. BioManager warns you at startup if it spots this.

Save the whole lab (Settings → Your data, admins) puts every record, account and uploaded file in one .biomanager file: a backup to carry, and the way to bring the lab to another computer (a new desktop app's first page: Bring a lab file here) or to a new server.

On a single computer, back up BioManager's data folder (~/Library/Application Support/Biomanager/ on a Mac, %APPDATA%\Biomanager\ on Windows, ~/.local/share/Biomanager/ on Linux) with Time Machine or File History. To put a backup back, quit BioManager, move data/biomanager.db aside and put the backup in its place (the guide's Restore a backup says how). Running from source, scripts/dbtool.py does the same:

python scripts/dbtool.py check                      # where is it, is it healthy, is it at risk
python scripts/dbtool.py backup                     # a consistent snapshot; keeps the last 30
python scripts/dbtool.py relocate ~/BioManagerData  # move it somewhere safe
python scripts/dbtool.py restore <file>

Upgrading is safe. Before a new version changes a database an older one made, it copies it (backups/before-upgrade-….db in the data folder; the last ten are kept), and every release is tested opening a demo lab made by each earlier release, with nothing lost. To go back, close BioManager, put that copy in place of data/biomanager.db and open the version it came from. A lab server takes a backup before every update.

A lab server backs itself up every night, checks every backup and test-restores one every week, with an optional off-site copy and a nightly copy on the admin's Mac. A desktop app that joins the lab keeps a copy of the lab on that computer (Settings → Devices & copies; a computer that shouldn't join can use a key from the server instead): checked when it arrives, refreshed daily, the newest 14 kept, and loadable into a new server if the old one is lost. Admins decide whether members may (guests never). An admin's copy is the whole lab; a member's holds what they can see in the app, without anyone's password, other people's private notebook pages, personal databases, personal to-dos and events, or the Audit log.

The lab's key locks the server's backups, Save the whole lab files and the copies on computers, so a file that leaks can't be read. The server and its admins' desktop apps hold it and open these files for you. Its recovery key (Settings → Your data → Lab key → Show the recovery key, admins) is the one way to open a backup if the server and every admin's computer are lost: keep it on paper or in a password manager, away from the backups. Settings → Your data → Export my data downloads your own mice, cages, weights, experiments, plasmids (each sequence as a GenBank file, with its features), notebook pages and profile as a zip at any time.

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📚 Documentation

Document	For
User guide	Using BioManager, step by step: setting up a lab, every module, phones, backups. Also under Help in the app's sidebar
deploy/README.md	Setting up a lab server: HTTPS, Tailscale, Google/Microsoft sign-in, backups, updates
deploy/RUNBOOK.md	Running a lab server: alerts, outages, restores, people joining and leaving
docs/GOOGLE_CALENDAR_SETUP.md	Connecting Google Calendar
docs/DEVELOPMENT.md	How BioManager is built: stack, styling, icons, the organism engine, access control, audit and undo, tests, security settings
docs/TESTING.md	How 1.0 was tested: six areas stress-tested like a lab and an attacker would, what was found and fixed, and the full reports

Working on BioManager itself? Start with docs/DEVELOPMENT.md. The test suite runs on SQLite and PostgreSQL with scripts/test.sh, on every push. To refresh these screenshots, see scripts/screenshots.py.

🙏 Licence and credits

BioManager is released under the MIT licence. If you use it in your research, Cite this repository on the GitHub page gives the citation in APA or BibTeX (from CITATION.cff).

Built with Python, Flask, SQLAlchemy, PostgreSQL / SQLite and Tailwind CSS. Icons from Font Awesome Free (CC BY 4.0) and game-icons.net by Delapouite (CC BY 3.0) — the mouse and fly are theirs; the plasmid, petri dish, cage, tank and culture-vial icons were drawn for this project. The people and records in the screenshots are made up.