Currently tutorial 12 (https://github.com/deepchem/deepchem/blob/master/examples/tutorials/12_Predicting_Ki_of_Ligands_to_a_Protein.ipynb) is failing with the following error on cell 8.

Loading raw samples now.
shard_size: 8192
About to start loading CSV from desc_canvas_aug30.csv
Loading shard 1 of size 8192.
---------------------------------------------------------------------------
A

We have a view of the metadata available for openworm repos deployed live here, driven by this code here.

At the moment metadata is shown in tabs, courtesy of @cheelee.

We'd like to add an alternate tabular view (possibly re-using some javascript/jquery grid) t

https://github.com/Revolutionary-Games/Thrive/blob/bf37ff573abcdafe05017db82999c9669449d83c/src/microbe_stage/Spawners.cs#L127

After showing BioJS to scientist at the Broad Institute, they realized that the DNA inside the logo is left-handed while DNA in nature is right-handed.

We should consider removing the DNA from the logo to stay consistent

I noticed in example code, some argument are inconsistent in the commented parts, such as lines in examples/molnet/train_molnet.py:
https://github.com/chainer/chainer-chemistry/blob/56e83dedb5de9dc9eb08ebf292be9ba76a4883ba/examples/molnet/train_molnet.py#L267-L274

args.gpu and concat_mols are not consistent with other codes and will throw errors. They should be modified to device and

Dear @kblin,

I would like to use ncbi-gneome-download as a python module within my pipeline and I have been having problems to decipher the arguments to pass to the download call. I guess the readme and documentation is not up to date or I am missing something.

For example, I tried on the command line and it worked fine for me the following code:

ncbi-genome-download -s genbank -F fast

There's an emerging standard for adding CITATION files to the root of a project to encourage academic citations.

We should add one to JB1.

Format spec: https://citation-file-format.github.io/

Have you checked the list of proposed tips to see if the tip has already been proposed?

• [ x] Yes

**Did you add yourself as a contributor by making a pull request if t

CodeCov looks like a good idea.

Seems really easy as we use Travis already. Are there other solutions?

We used to use emma, but I think that's been lost when we moved to gradle from ant.

If the data changes sign, then the fold and log(fold) say (nd). Explain this in the docs.

Also, python docs can be improved:

• Annoying, and confusing, to jump back to JavaScript docs for kwargs definitions
• Need an example for comparison data
• Putting docs in example notebooks is not ideal. Get the Python stuff into readthedocs.

We can definitely increase the number of our premade lifeforms in Seagull. I only started with a few, but in LifeWiki there seems to be a lot more!

Will need some help on this, any takers? You can add 1 or 2 from LifeWiki, I can help you along the way! https://conwaylife.com/wiki/Main_Page

How to start

Choose a fun Lifeform from LifeWiki: https://conwaylife.com/wiki/Main_Page then co

Figure out a way to package up all the markdown wiki pages with the repository and pretty-print them out as an extended help option.

$: sb -btr -h

I will need to write a script to convert the markdown to something that looks nicer in the terminal.

Line 876 in the main file - If you want to add a syringe that is not one of the BD syringes, you must edit lines 874, 875, 876. Line 876 has self.syringe_areas but I don't know what the units are. mm^2? I'd add an inline comment with the units, for example,

self.syringe_areas = [17.34206347, 57.88559215, 112.9089185, 163.539454, 285.022957, 366.0961536, 554.0462538] # mm^2

(Might also be

The indra/tools/expand_families.py file should be moved to indra/preassembler. We will need to track down where it's used in other repos and fix imports. It should also be properly documented.

Is there anyway to display the figures you have below the code in the pictures below, or did you just draw this out by hand? Some of my assemblies are being weird/I am trying to learn the package, and it would be useful for troubleshooting and general purpose if the ascii figures were built in attributes for both common_sub_strings and terminal_overlap.

![image](https://user-images.githubuserco

Describe the bug
When trying to download *.txt document from the pipeline DOCUMENTS tab - the downloaded file contains error instead of the document content

To Reproduce
Steps to reproduce the behavior:

1. Open any pipeline, select the DOCUMENTS tab
2. Upload the document with txt extension
3. Click the Download button next to the uploaded document (or click the doc

Description

Formatted output of some code examples are missing/not parsed correctly anymore. see this example from the BioItems docs :

As outlined in https://docs.google.com/document/d/1cKcQfx8X8uAXR6JF96jqZO8OCpwwkYatnxSIyVXvYbo/edit# , we'd like to start using hexastore-like method to encode triples in key-value Zenodo annotations. Suggest to pick two examples, one simple, one complex and add them to Zenodo for GloBI to index.

fyi - @mguidoti @slint