Roadmap ideas

[BjornFJohansson]

barcode library print barcodes on labels
free Proof of Posting Certificates
protein analysis
analyze growth on solid medium

[BjornFJohansson]

growth rate modelling
https://en.wikipedia.org/wiki/Logistic_function#In_ecology:_modeling_population_growth
http://stackoverflow.com/questions/4308168/sigmoidal-regression-with-scipy-numpy-python-etc
http://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=1330&context=gradreports
http://www.math.usu.edu/~powell/ysa-html/ysa-html.html
http://aem.asm.org/content/77/8/2772.full

http://mattoc.com/read-xlsx-with-xlrd.html
http://nbviewer.jupyter.org/gist/rossant/9463955 qgrid

[BjornFJohansson]

Visualization of DNA molecules:
https://pypi.python.org/pypi/giraffe/2.0
https://github.com/ikravchuk/json2angularplasmid
https://github.com/mengqvist/DNApy
https://www.biostars.org/p/94400/
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc252

[BjornFJohansson]

Gel analysis
google
PyElph

https://pypi.python.org/pypi/gelutils

[BjornFJohansson]

Annotation of DNA sequences:
http://www.vicbioinformatics.com/software.prokka.shtml
http://wishart.biology.ualberta.ca/PlasMapper/
https://www.biostars.org/p/188955/
https://biosustain.github.io/goodbye-genbank/

[BjornFJohansson]

simplify download from more sources:
https://pypi.python.org/pypi/simplegist/1.0.1

possibly add a download function from addgene?

import requests
from lxml import html
r = requests.get('https://www.addgene.org/13744/sequences/')
tree = html.fromstring(r.text)
rawdata_addgene_full_sequence = tree.xpath(".//*[@id='depositor-full']")
pGL_MLKif3B = pydna.read( rawdata_addgene_full_sequence[0].text_content() ).looped()
rawdata_addgene_partial_sequence = tree.xpath(".//*[@id='addgene-partial']")
pGL_MLKif3B_partial = pydna.read( rawdata_addgene_partial_sequence[0].text_content() )

[BjornFJohansson]

Notes

before new release 1.2.0

• add docstrings to design module
• add warnings for old functions in design.py
• add a find method to Dseqrecords that can find over the edge and otherwise work like str.find "abcde".find("c") ->2 "abcde".find("v") -> -1
• update changelog

https://github.com/BjornFJohansson/pydna/issues

[file:///home/bjorn/files/ARCHIVE/2015-06-17/pydna papers]

http://www.biomedcentral.com/1471-2105/11/9
http://www.biomedcentral.com/1471-2105/10/258
http://www.biomedcentral.com/1471-2105/7/10

Documentation http://pydna.readthedocs.org/
Discussion group https://groups.google.com/d/forum/pydna

todo before publication:

1. write tests√

2. tests should be runnable by python setup.py test√

3. better docstrings√

4. a site using pydoc or Epydoc (Read the docs)√

5. a cookbook/tutorial with example code√

6. a title "pydna: Python tools for cloning at the command line"
   "pydna: Executable documentation for cloning strategies in Python"√

7. A good motivation as to why this should be published
   Executable documentation
   compare BioCoder

8. A journal! Journal of Biological Engineering published Biocoder paper above!
   and http://www.jbioleng.org/content/3/1/19 TinkerCell: modular CAD tool for synthetic biology
   impact factor 3.88

9. An Idea about the style:
   Inspiration:
   http://www.ncbi.nlm.nih.gov/pubmed/19304878?dopt=Abstract biopython paper was cited by:
   http://www.ncbi.nlm.nih.gov/pubmed/21210978 An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.
   http://www.ncbi.nlm.nih.gov/pubmed/20041221 A quick guide for developing effective bioinformatics programming skills.
   http://www.ncbi.nlm.nih.gov/pubmed/12230038 The Bio* toolkits--a brief overview.
   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365/ Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
   http://www.ncbi.nlm.nih.gov/sites/entrez/21059251?dopt=Abstract&holding=f1000,f1000m,isrctn Biocoder: A programming language for standardizing and automating biology protocols

Executable Documentation in general

Why is so much documentation worthless? Wouldn't is be nice if your
documentation actually reflected what your system does? One way to do this is
to create what is being called executable documentation or executable
specifications. If you are struggling with ambiguous requirements, lack of
contact with the business, or a chasm between development and testing, this
session is for you. What is executable documentation? Simply put, instead of
adding more details to requirements, capture the desired system behavior in
acceptance testing tools which are accessible to the entire project community.
The session will focus on FIT, but it may include other tools for creating ED.
History has shown me that ED - requirements that have two states (green and
red) - helps project communities consistently create better software, faster!

##Abstract

Reproducibility is a key component of a scientific experiment.

Biological protocols are often ambiguously described.

There are examples of attempts to formalize biological protocols.

BioCoder is such and example.

DNA constructions are often incompletely described.

Following described cloning strategies lead to ambiguous results.

Such as Mumberg vectors.

This is a special case of a more fundamental problem arising from the
separation of specification (the protocols or the strategy) and the execution
(what was actually done).

In the case of cloning strategies, sometimes the theoretical sequences are
assembled In-silico and the result is submitted to an public database such as
genbank.

While better than nothing, the strategy is not preserved in the final result,
intervening steps are not preserved.

There is a related problem

pydna was developed to include tools to describe double stranded DNA and the most common
unit operations performed to manipulate DNA.

The outcome of each unit operation is simulated, rather than the physical or chemical processes.

The python code describing the steps of a cloning strategy is a compact, self
contained, unambigous description of the experiment, where each intermediate
result is automatically generated as a part of the strategy.

The content of a directory can be digitally signed to preserve the integrity of the content.

DNA manipulations can be divided into well defined unit operations including:
PCR
Filling in with klenow
DNAse treatment
Restriction digestion
intermolecular ligation
intramolecular ligation
homologous recombination (yeast gap repair)
site specific recombination (Gateway)
methylation

BMC Bioinformatics
PLoS Comput Biol
Brief Bioinform
J Biol Eng

[hsiaut]

Hey Bjorn,
Just to add to your list of annotation ideas:
I've always wanted a better way of annotating plasmid sequences; most tools today use a DNA exact match, but a simple extension would be to do an amino acid match against a feature database. A lot of plasmid annotation comes down to manual and iterative blast searching, some of which surely could be automated.

genolib was one effort to get at a more standardized way of annotation.
https://academic.oup.com/nar/article/43/10/4823/2409072/GenoLIB-a-database-of-biological-parts-derived

I also have a paper from grad school where we looked at trying to catch some issues in designing plasmids.

http://pubs.acs.org/doi/abs/10.1021/sb400176e

Thanks & feel free to ignore if this comment is unwanted,
Tim

[BjornFJohansson]

Hi Tim,
Great suggestions! Your web form looks like a good way of checking final results.
However, I tried the examples and they didn't come back with a result yet, are they still online?

The NAR paper looks as a good source for gold standard features. I contacted the author about it, since I couldn't download the suppl data from the NAR website.

[hsiaut]

Hi Bjorn,
I think the website no longer works and I graduated a while ago.

https://github.com/hsiaut/EDSSI has the source code.

Thanks for checking those links out,
Tim

[BjornFJohansson]

https://academic.oup.com/nar/article/43/10/4823/2409072/GenoLIB-a-database-of-biological-parts-derived

email conversation:

---

Dear Dr. Peccoud,
I was not able to download the supplementary data from your recent NAR paper on GenoLIB.
I probably should have contacted the journal for this, but I could find not relevant contact for this.

For me the link:
https://academic.oup.com/nar/article/43/10/4823/2409072/GenoLIB-a-database-of-biological-parts-derived?searchresult=1#supplementary-data

redirects to the front page of the article and does not download anything. Not sure if this is a problem on my side.

Thanks,
Bjorn Johansson

---

Bjorn,

The data is now hosted on GenoCAD.com. You can create an account to navigate the dataset, customize it, and potentially export it.

Let me know if you run into issues.

Jean

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https://en.wikipedia.org/wiki/GenoCAD

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Genocad.com seems down on 3 May 2017

[BjornFJohansson]

https://penandpants.com/2012/03/09/reading-text-tables-with-python/

[BjornFJohansson]

https://github.com/Edinburgh-Genome-Foundry/BandWagon

[marcus-r-kelly]

Do you feel that incorporating Gateway cloning reactions would be a good fit for this project? If so I would love to see that in a future release.

[BjornFJohansson]

I have started preparation to implement gateway cloning already. I have never used it myself, but it seems popular.

[marcus-r-kelly]

Great to hear, thank you!

…

On Tue, Oct 27, 2020 at 6:18 AM Björn Johansson ***@***.***> wrote: I have started preparation to implement gateway cloning already. I have never used it myself, but it seems popular. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#27 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFZZSKOBYALV6GZCMZGFRLSM3CCXANCNFSM4CUQFPVA> .

-- Mark