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freezerbox-0.9.0
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مشاهده بیشترتوضیحات
Database of DNA sequences.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | freezerbox-0.9.0 |
| نام | freezerbox |
| نسخه کتابخانه | 0.9.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | Kale Kundert <kale@thekunderts.net> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/freezerbox/ |
| مجوز | - |
**********
FreezerBox
**********
.. image:: https://img.shields.io/pypi/v/freezerbox.svg
:alt: Last release
:target: https://pypi.python.org/pypi/freezerbox
.. image:: https://img.shields.io/pypi/pyversions/freezerbox.svg
:alt: Python version
:target: https://pypi.python.org/pypi/freezerbox
.. image:: https://img.shields.io/readthedocs/freezerbox.svg
:alt: Documentation
:target: https://freezerbox.readthedocs.io/en/latest/?badge=latest
.. image:: https://img.shields.io/github/workflow/status/kalekundert/freezerbox/Test%20and%20release/master
:alt: Test status
:target: https://github.com/kalekundert/freezerbox/actions
.. image:: https://img.shields.io/coveralls/kalekundert/freezerbox.svg
:alt: Test coverage
:target: https://coveralls.io/github/kalekundert/freezerbox?branch=master
.. image:: https://img.shields.io/github/last-commit/kalekundert/freezerbox?logo=github
:alt: GitHub last commit
:target: https://github.com/kalekundert/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 <https://github.com/kalekundert/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...
نیازمندی
| مقدار | نام |
|---|---|
| - | byoc |
| - | autoprop |
| - | autosnapgene |
| - | biopython |
| - | docopt |
| - | entrypoints |
| - | exmemo |
| - | inform~=1.21 |
| - | mako |
| - | mergedeep |
| - | more_itertools~=8.0 |
| - | natsort |
| - | networkx |
| - | numpy |
| - | pandas |
| - | parsy |
| - | rtoml |
| - | sklearn |
| - | stepwise~=0.23 |
| - | stringcase |
| - | tidyexc |
| - | tqdm |
| - | voluptuous |
| - | sphinx |
| - | sphinx_rtd_theme |
| - | autoclasstoc |
| - | pytest |
| - | pytest-cov |
| - | coveralls |
| - | parametrize_from_file |
| - | pytest_tmp_files |
| - | re_assert |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| ~=3.8 | Python |
نحوه نصب
نصب پکیج whl freezerbox-0.9.0:
pip install freezerbox-0.9.0.whl
نصب پکیج tar.gz freezerbox-0.9.0:
pip install freezerbox-0.9.0.tar.gz