BioManager 1.0.6

BioManager 1.0.6

New

• BioManager in Chinese (中文). Choose Settings → Language, or 中文 / English on the sign-in page. Without a choice, BioManager follows the language your browser or computer asks for first.
  • Translated so far: the sidebar and menus, Home, the mouse colony with its cage panel and dialogs, the sheets, the calendar, cage cards and Settings.
  • Still in English: the other databases' pages, and the messages BioManager shows after you save or change something. They are next.
  • What your lab typed (names, notes, strains) always stays as typed.
• The website is in Chinese too: biomanager.org/zh/, with the user guide and the server page.

Fixed

• Windows set to Chinese, Japanese or Korean: the desktop app starts again. Since 0.10.2 it closed at once, before any window opened, on Windows 10 and 11 alike.
  • If BioManager never opened for you on Windows, download 1.0.6 below. Your data was never touched.

Updating

• Desktop app: Install and Restart when it offers 1.0.6, or download it below. Your data is kept outside the app, and a copy is taken before the database is upgraded.

  • On a Chinese, Japanese or Korean Windows, where 1.0.5 doesn't start, download 1.0.6 below, unpack the whole folder and open BioManager.exe in it.

• Lab server:

  1. Take a fresh backup (docker compose exec backup backup.sh).
  2. Unpack the new biomanager-server.tar.gz over the old folder. Your .env, backups and certificates are kept.
  3. Run host/load-image.sh, then docker compose up -d --build.

  Nothing in the database changes in this release. Details are under Updating the app in the runbook (deploy/RUNBOOK.md in the bundle).

---

Download the file for your device below, or from the website.

File	For
BioManager-macOS-AppleSilicon.zip	Macs with an M1 or later chip
BioManager-macOS-Intel.zip	Macs with an Intel chip
BioManager-Windows.zip	Windows 10 and 11, 64-bit
BioManager-Linux.AppImage	Linux, x86-64: mark it executable and open it
BioManager-Linux.tar.gz	Linux, the same app as a folder
BioManager-Android.apk	Android 7 and later: connects to your lab's BioManager server
biomanager-server.tar.gz	A lab server: the deploy files. How to set one up
biomanager-image-amd64.tar.gz	The lab server's app for Intel/AMD machines, loaded by the bundle's host/load-image.sh
biomanager-image-arm64.tar.gz	The same for ARM machines, such as Oracle Cloud's free Ampere VMs

First launch: on a Mac, right-click BioManager and choose Open; on Windows, choose More info → Run anyway. The apps are not signed by Apple or Microsoft, so the system asks once. On Android, allow your browser to install apps when asked.

Your data is kept outside the app, so updating never touches it.

BioManager 1.0.5

BioManager 1.0.5

What works differently

• BioManager's website is now biomanager.org. Help → User guide, the desktop app's About box, the server set-up page and the app's other links go there.
  • The old address still works: it sends you to the new one.

Updating

• Desktop app: Install and Restart when it offers 1.0.5, or download it below. Your data is kept outside the app, and a copy is taken before the database is upgraded.

• Lab server:

  1. Take a fresh backup (docker compose exec backup backup.sh).
  2. Unpack the new biomanager-server.tar.gz over the old folder. Your .env, backups and certificates are kept.
  3. Run host/load-image.sh, then docker compose up -d --build.

  Nothing in the database changes in this release. Details are under Updating the app in the runbook (deploy/RUNBOOK.md in the bundle).

---

Download the file for your device below, or from the website.

File	For
BioManager-macOS-AppleSilicon.zip	Macs with an M1 or later chip
BioManager-macOS-Intel.zip	Macs with an Intel chip
BioManager-Windows.zip	Windows 10 and 11, 64-bit
BioManager-Linux.AppImage	Linux, x86-64: mark it executable and open it
BioManager-Linux.tar.gz	Linux, the same app as a folder
BioManager-Android.apk	Android 7 and later: connects to your lab's BioManager server
biomanager-server.tar.gz	A lab server: the deploy files. How to set one up
biomanager-image-amd64.tar.gz	The lab server's app for Intel/AMD machines, loaded by the bundle's host/load-image.sh
biomanager-image-arm64.tar.gz	The same for ARM machines, such as Oracle Cloud's free Ampere VMs

First launch: on a Mac, right-click BioManager and choose Open; on Windows, choose More info → Run anyway. The apps are not signed by Apple or Microsoft, so the system asks once. On Android, allow your browser to install apps when asked.

Your data is kept outside the app, so updating never touches it.

BioManager 1.0.4

BioManager 1.0.4

New

• What's new, once after each update. The first page you open after BioManager is updated shows a short note: what is new, what works differently, and what was fixed, with a link to the full release notes.
  • Got it puts it away for good. Help → What's new opens it again.
  • If you skipped a version, you see the notes of each version since the last one you saw.
  • A new account sees the welcome tour instead.

What works differently

• Litter born (it was Litter born today) asks for the date of birth before recording the litter.
  • The date starts as today; change it for a litter you found a day or two late.
  • A date in the future is refused.
  • If the cage already has a litter recorded, it says the new date replaces it.
• The colony, the admin Colony overview and printed cage cards say Shared for any shared cage, not only breeder cages.

Fixed

• In an open cage, the header of the cage's mouse table no longer covers its first mouse.
• Windows 10: the desktop app no longer opens a blank or broken window on a PC without Microsoft Edge WebView2, the part of Windows its window uses.
  • It offers to download WebView2 from Microsoft and opens in your web browser meanwhile. Leave its message open while you use it.
  • Once WebView2 is installed, open BioManager again and it has its own window.
  • If the window can't open for another reason, it says why and opens in the browser too.
• On Windows, the window no longer fails to open because Windows marked the app's files as downloaded from the internet.

Updating

• Desktop app: Install and Restart when it offers 1.0.4, or download it below. Your data is kept outside the app, and a copy is taken before the database is upgraded.

• Lab server:

  1. Take a fresh backup (docker compose exec backup backup.sh).
  2. Unpack the new biomanager-server.tar.gz over the old folder. Your .env, backups and certificates are kept.
  3. Run host/load-image.sh, then docker compose up -d --build.

  The database upgrades itself on start; every earlier release's database was checked to upgrade with nothing lost. Details are under Updating the app in the runbook (deploy/RUNBOOK.md in the bundle).

---

Download the file for your device below, or from the website.

File	For
BioManager-macOS-AppleSilicon.zip	Macs with an M1 or later chip
BioManager-macOS-Intel.zip	Macs with an Intel chip
BioManager-Windows.zip	Windows 10 and 11, 64-bit
BioManager-Linux.AppImage	Linux, x86-64: mark it executable and open it
BioManager-Linux.tar.gz	Linux, the same app as a folder
BioManager-Android.apk	Android 7 and later: connects to your lab's BioManager server
biomanager-server.tar.gz	A lab server: the deploy files. How to set one up
biomanager-image-amd64.tar.gz	The lab server's app for Intel/AMD machines, loaded by the bundle's host/load-image.sh
biomanager-image-arm64.tar.gz	The same for ARM machines, such as Oracle Cloud's free Ampere VMs

First launch: on a Mac, right-click BioManager and choose Open; on Windows, choose More info → Run anyway. The apps are not signed by Apple or Microsoft, so the system asks once. On Android, allow your browser to install apps when asked.

Your data is kept outside the app, so updating never touches it.

BioManager 1.0.3

The files for this version are no longer attached. Download the newest version from the latest release; a lab server can also go back to this version with git checkout v1.0.3.

BioManager 1.0.3

New

• Project groups (More → Project groups): some of the lab working on one project.
  • An admin makes a group and picks its members. A group's leads can add and take out members. Someone can be in several groups.
  • Wherever you could share something with the lab, you can share it with one of your groups instead. A cage, plasmid, reagent, breeding tank or lab stock vial shared with a group is its members' to edit. Everyone in the lab still sees it.
  • A database made for a group (Who is it for? when you add one) is seen only by its members and admins. Share with the group on the Databases page gives one of your own databases to a group.
  • A notebook page can be shared with a group, to view or to edit, and a template can be for a group.
  • My groups, beside My colony, shows the mice and cages of everyone in your groups.
  • Deleting a group makes what was shared with it its owner's own again.
• Who sees it, on calendar events and to-dos: Only me, Everyone in the lab, or one of your groups.
  • Your own events and to-dos are seen by nobody else, admins included.
  • A shared event can be changed only by the person who added it and admins.
  • A shared to-do can be ticked off by anyone it is for.
  • A new event starts as the lab's, a new to-do as yours.
• Any cage can be shared, by its owner or an admin, with the lab or a group.
  • A Breeder cage starts shared. Every other cage starts personal, and a cage that stops being a breeder cage goes back to personal.
  • The Cages tab has a chip for each purpose (Experiments, Breeder…) to show only those cages.
• Settings → Devices shows which device holds the lab's master copy, and every computer linked to the lab.
  • A desktop app linked to the lab's server can Open the lab in this window, to work on the shared lab in the app.
  • A desktop can Share this lab on the network, for the other computers on the same network.
  • An admin can Make it the master, handing the master copy to a linked desktop. The other device turns read only and points everyone there. Give the master copy back returns it.
  • Nothing is ever merged: there is one master copy at a time.

What works differently

• Other people's to-dos are no longer on your calendar. Each person's own to-dos are theirs. Use a lab or group to-do for work that others should see.
• Only its owner, or an admin, changes or deletes a calendar event. Before, anyone could.
• Away soon lists only someone's shared to-dos, not their personal ones.
• A sample whose source is a mouse number too big for the database is now saved with the usual "no mouse" warning. Before, on a lab server, the sample was refused and the samples sheet could stop opening.

Updating

• Desktop app: Install and Restart when it offers 1.0.3, or download it below. Your data is kept outside the app, and a copy is taken before the database is upgraded.

• Lab server:

  1. Take a fresh backup (docker compose exec backup backup.sh).
  2. Unpack the new biomanager-server.tar.gz over the old folder. Your .env, backups and certificates are kept.
  3. Run host/load-image.sh, then docker compose up -d --build.

  The database upgrades itself on start; every earlier release's database was checked to upgrade with nothing lost. Every event the lab already has stays shared with the lab, and existing to-dos become their owners'. Details are under Updating the app in the runbook (deploy/RUNBOOK.md in the bundle). If the app ever says it is read only, see The app says it is read only there.

BioManager 1.0.2

The files for this version are no longer attached. Download the newest version from the latest release; a lab server can also go back to this version with git checkout v1.0.2.

BioManager 1.0.2

New

• Sheets you read at a glance, in every database:
  • The page scrolls, not the sheet. The search, chips and buttons stay at the top of the window, with the column names under them. The count and pages stay at the bottom. All per page lists every row on one page.
  • Text is smaller and columns are tighter, so more fits across without scrolling sideways.
• New, at the bottom left, adds an empty row at the end of the sheet, with its first cell ready to type in.
  • A strain, fish, fish line, plasmid or order needs a name or a tank first, so there the button opens its form.
• The dot shows an animal's age:
  • blue for young, green for adult, red for old;
  • mice: under 8 weeks, 8 to 30 weeks, past 30 weeks;
  • fish: under 3 months, up to 18 months, past 18 months;
  • vials and plates: progeny still developing, adults, past the flip or chunk;
  • grey once an animal is not alive. Point at a dot to see what its colour means.
• Expired reagents, antibodies and viruses are red: the dot, the number and the name, as well as the date.
• Cages:
  • Litter born and Wean due come right after the mice, so when to wean is always in view.
  • Type over a cage's number to renumber it. Its mice go with it, and a number another cage has is refused.
• Sequence, beside each plasmid's number, opens its sequence and map. A plasmid with none yet shows Add sequence.

What works differently

• New litters are numbered L-1, L-2, L-3…, one past the highest L-number the lab has. The litter sheet sorts them by number, so L-2 comes before L-10. Litters you named another way keep their names.
• Every database has a name of its own. A name another database has, in any case and including Mouse colony, Zebrafish and Plasmids, is refused when you create or rename one. This way @ and a database's name in a notebook page always mean one database. Databases that already share a name keep it until one is renamed.
• Table, Boxes and List for plasmids, and Table, Rack grid and Genotyping queue for fish tanks, now sit above the sheet, where every database has them.
• A cage's number is now typed in rather than clicked. Its arrow, or its mice count, opens the cage.
• Hidden columns and widths you set on the Cages tab are reset once, because its columns moved.

Updating

• Desktop app: Install and Restart when it offers 1.0.2, or download it below. Your data is kept outside the app.

• Lab server:

  1. Take a fresh backup (docker compose exec backup backup.sh).
  2. Unpack the new biomanager-server.tar.gz over the old folder. Your .env, backups and certificates are kept.
  3. Run host/load-image.sh, then docker compose up -d --build.

  There is no database change this time. Details are under Updating the app in the runbook (deploy/RUNBOOK.md in the bundle).

BioManager 1.0.1

The files for this version are no longer attached. Download the newest version from the latest release; a lab server can also go back to this version with git checkout v1.0.1.

BioManager 1.0.1

New

• An Experiments tab in every animal database: Zebrafish, fly and worm
  stocks and the lab's organism databases now have Experiments beside
  their tanks, fish and clutches (or stocks, or records), working as the
  mouse colony's does: put animals under a shared treatment plan, record
  what is done each day and follow a readout suited to the animal (or your
  own). A new experiment can start with all the animals of a tank, rack or
  housing.
• Cages show their mice again: on the Cages tab every cage opens with
  its mice beneath it, ready for weaning, moving and the rest. Close all
  / Open all folds them and is remembered; the arrow, the cage's number
  or its mice count opens one. Cards shows each cage as its own card.

What works differently

• Only Breeder cages are shared with the lab. A Breeder cage starts
  shared, and its owner (or an admin) can make it personal. Other cages
  are their owner's: on updating, a Breeding or Stock cage that was marked
  shared becomes personal, and Breeder cages that were shared stay so.
  Admins still see every cage.

Updating

• Desktop app: Install and Restart when it offers 1.0.1, or download
  it below. Your data is kept outside the app and a copy is taken before
  the database is upgraded.
• Lab server: take a fresh backup (docker compose exec backup backup.sh),
  unpack the new biomanager-server.tar.gz over the old folder (your .env,
  backups and certificates are kept), then host/load-image.sh and
  docker compose up -d --build. The database upgrades itself on start;
  every earlier release's database was checked to upgrade with nothing
  lost. Details: Updating the app in the runbook (deploy/RUNBOOK.md in
  the bundle).

BioManager 1.0.0

The files for this version are no longer attached. Download the newest version from the latest release; a lab server can also go back to this version with git checkout v1.0.0.

BioManager 1.0

The first version we call finished: tested for weeks as whole labs would use
it, by a mouse lab, a fish, fly and worm lab and a wet lab doing cloning,
cell culture, protein and RNA work, and by testers trying to break it. How
it was tested, and what they found and what was fixed, is in
How BioManager 1.0 was tested.

New

• Utilities: 41 bench calculators, answering as you type: molarity,
  dilutions and serial dilutions, percent and ×-fold stocks, buffer pH,
  osmolarity; A₂₆₀, DNA moles and copies, oligo Tm, ligation and Gibson,
  PCR and qPCR master mixes, qPCR efficiency, ΔΔCt; A₂₈₀, protein MW, ε and
  pI from the sequence, BCA and Bradford standard curves, SDS-PAGE recipes;
  cell counts, seeding, doubling time, transfection, MOI, lentivirus titer,
  freezing down; OD₆₀₀, antibiotics, rpm ↔ × g, doses by body weight,
  agarose gels, radioactive decay, statistics and units. Reference tables
  for vessels, buffers, antibiotics, gels, isotopes and molecular weights.
• Customize Home: choose which cards Home shows, their order and width,
  and add your to-dos, instrument bookings, recent pages and calculators.
• Primers & oligos and Cell lines databases, ready-made.
• @links to any record in a notebook page (@antibodies 5), found by
  name, catalogue number or lot; the chip shows the record's name, and the
  record lists the pages that link it (Used in notebook pages).
• Numbers for results: concentration and purity on samples and plasmid
  tubes, pasted straight from a Nanodrop column into the sheet.
• Positions that look after themselves: Add many fills a box side by
  side, a used-up tube frees its place, moving a box updates Stored at.
• Repeating and duplicated bookings, instruments you can rename, and
  calendar repeats such as the first Monday of the month.
• Templates that keep a page's type and can keep only its structure;
  labels where you choose what each says; A₂₈₀ in the calculator block;
  Order again that says when something is already on order.

What works differently

• BioManager now sends its makers anonymous counts, once a day. Earlier
  versions asked in the setup survey but never sent anything; from 1.0, a
  lab that left Send BioManager's makers anonymous counts ticked sends
  one short message a day: the version, desktop app or server, the
  operating system and database, how many members and how many were active
  this week (as ranges), which functions are on and how many databases of
  each kind, and a random id for the installation. Never names, email
  addresses, anything anyone wrote, what your databases are called, or the
  computer's name or address, and where it came from is not kept. An admin
  sees exactly what is sent, and can Switch off, under Feedback →
  Usage report. On a lab server, BIOMANAGER_TELEMETRY=0 (or
  DO_NOT_TRACK=1) in .env turns it off for good.
• The sidebar's foot is shorter: More holds Batch history and the
  admin pages (Lab setup, Colony overview, Audit log, Manage users, Guests,
  Racks & boxes); Help holds the user guide and Send feedback.
• A plasmid's page is at its number: plasmid #12 is …/plasmid/12. Old
  links (…/plasmids/19) still open the right plasmid.
• Renaming a database changes its address to the new name. The old
  address keeps working, so printed labels, bookmarks and @mentions in
  notebook pages still find it.
• A page started with a topic open goes in that topic, and in Inbox
  when none is; search puts names that start with what you typed first,
  and a lot or catalogue number typed in full before them; times on
  notebook pages are on the lab's clock.
• A sheet keeps your sort after a reload, and its chip is in the address
  (?chip=…), so a bookmark opens it the same way.

Updating

• Desktop app: Install and Restart when it offers 1.0.0, or download
  it below. Your data is kept outside the app and a copy is taken before
  the database is upgraded.
• Lab server: take a fresh backup (docker compose exec backup backup.sh),
  unpack the new biomanager-server.tar.gz over the old folder (your .env,
  backups and certificates are kept), then host/load-image.sh and
  docker compose up -d --build. The database upgrades itself on start
  (the log says Upgrading the database from … to …); every earlier
  release's database was checked to upgrade with nothing lost. Details:
  Updating the app in the runbook (deploy/RUNBOOK.md in the bundle).

Known limits

Things the labs asked for that come after 1.0: linking a sample to what is
made from it (RNA → cDNA → plate), @links to fly vials and organisms, a cell-culture database with Passage
actions, booking a chain of instruments at once, freezer and equipment
logs, and a qPCR plate-layout block.

BioManager 0.10.1

Download the file for your device below, or from the website.

File	For
BioManager-macOS-AppleSilicon.zip	Macs with an M1 or later chip
BioManager-macOS-Intel.zip	Macs with an Intel chip
BioManager-Windows.zip	Windows 10 and 11, 64-bit
BioManager-Linux.AppImage	Linux, x86-64: mark it executable and open it
BioManager-Linux.tar.gz	Linux, the same app as a folder
BioManager-Android.apk	Android 7 and later: connects to your lab's BioManager server
biomanager-server.tar.gz	A lab server: the deploy files. How to set one up
biomanager-image-amd64.tar.gz	The lab server's app for Intel/AMD machines, loaded by the bundle's host/load-image.sh
biomanager-image-arm64.tar.gz	The same for ARM machines, such as Oracle Cloud's free Ampere VMs

First launch: on a Mac, right-click BioManager and choose Open; on Windows, choose More info → Run anyway. The apps are not signed by Apple or Microsoft, so the system asks once. On Android, allow your browser to install apps when asked.

Your data is kept outside the app, so updating never touches it.