FreezerBox
FreezerBox is a tool for keeping track of biochemistry lab reagents such as plasmids, oligos, proteins, buffers, etc. It emphasizes keeping track of how each construct was made, and aims to be compatible with existing reagent-management systems.
Example
Your want a tool to better manage your plasmids, but you don’t want to spend a bunch of time re-entering the information for your existing plasmids, which is stored in a big Excel spreadsheet. After installing FreezerBox, you quickly configure it to recognize the column headers in your spreadsheet. Nothing about your existing spreadsheet needs to change.
You just designed primers to clone a new plasmid. You enter both the primers and the plasmid into your spreadsheet. While it’s fresh in your head, you also describe how the plasmid will be made in a column labeled “Construction”. The description might look like:
INV: template=p2 primers=o2,o3
This syntax indicates that the plasmid is constructed by inverse PCR (“INV”) using the plasmid “p2” as a template and the oligos “o1” and “o2” as primers.
You just received the primers you designed last week, but you don’t remember exactly how you were planning to use them. You use FreezerBox—in conjunction with stepwise—to generate an protocol specifying all the relevant details: volumes, concentrations, construct names, etc. If you are making several constructs, the protocol will even group similar constructs and create master mixes of common reagents when possible:
$ stepwise make p3 March 27, 2020 $ stepwise make p3 1. Prepare 10x primer mix [1]: Reagent Stock Volume ───────────────────────── o2 100 µM 0.50 µL o3 100 µM 0.50 µL water 9.00 µL ───────────────────────── 10.00 µL 2. Setup 1 PCR reaction and 1 negative control [2]: Reagent Stock Volume ───────────────────────────────── water 3.00 µL p2 20 pg/µL 1.00 µL primer mix 10x 1.00 µL Q5 master mix 2x 5.00 µL ───────────────────────────────── 10.00 µL 3. Run the following thermocycler protocol: - 98°C for 30s - Repeat 35x: - 98°C for 10s - 60°C for 20s - 72°C for 3 min - 72°C for 2 min 4. Run 1 ligation reaction: Reagent Stock Volume ──────────────────────────────────── water 6.75 µL T4 ligase buffer 10x 1.00 µL T4 PNK 10 U/µL 0.25 µL T4 DNA ligase 400 U/µL 0.25 µL DpnI 20 U/µL 0.25 µL PCR product 50 ng/µL 1.50 µL ──────────────────────────────────── 10.00 µL - Incubate at room temperature for 1h. Notes: [1] For resuspending lyophilized primers: 100 µM = 10 µL/nmol [2] For diluting template DNA to 20 pg/µL: Dilute 1 µL twice into 7*sqrt(DNA) µL
Installation
Install FreezerBox using pip:
$ pip install freezerbox
Usage
More details coming soon…
1 maintainer
Metadata
1 maintainer
Release files for freezerbox 0.26.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| freezerbox-0.26.0.tar.gz | 142.6 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| freezerbox-0.26.0-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details |
Total release size: 183.6 kB
Release files / freezerbox-0.26.0.tar.gz
| Download URL | freezerbox-0.26.0.tar.gz |
|---|---|
| Size | 142.6 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
917afa90586847514455a13c12ed792574022515a51c206b191779c86de038e3
|
|
BLAKE2b-256 checksum How to use checksums |
a81003b0065da5fc4373ed3943e579d2f03e7f9a38f43b83a2c0cfd8671ae25d
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.8.3 readme-renderer/37.1 requests/2.28.1 requests-toolbelt/0.9.1 urllib3/1.26.12 tqdm/4.64.1 importlib-metadata/4.12.0 keyring/23.9.1 rfc3986/2.0.0 colorama/0.4.5 CPython/3.9.13
|
Release files / freezerbox-0.26.0-py2.py3-none-any.whl
| Download URL | freezerbox-0.26.0-py2.py3-none-any.whl |
|---|---|
| Size | 40.9 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
541cb829bd249c0d24ba125a8e4525b25ecead95792c59980e55a62b90d1f623
|
|
BLAKE2b-256 checksum How to use checksums |
bbb30a1f0e033fe92aac8ab7b23cdb82cba73b2d845f2c67679d13e329680081
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.8.3 readme-renderer/37.1 requests/2.28.1 requests-toolbelt/0.9.1 urllib3/1.26.12 tqdm/4.64.1 importlib-metadata/4.12.0 keyring/23.9.1 rfc3986/2.0.0 colorama/0.4.5 CPython/3.9.13
|
Security for freezerbox 0.26.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
