# Guide to choosing a Theory project

*July 5-23, 2021*

Pure theory projects are usually pursued by more advanced students. If your group is relatively new to neuroscience, you should consider doing a dataset project *and* include a theory component to it.

Every group can bring up and discuss theory projects. We have two example project templates for this that include code. However, a theory project can go in any direction.

## Working memory

|   | Run | View |
| - | --- | ---- |
| Working memory | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/NeuromatchAcademy/course-content/blob/main/projects/theory/RNN_working_memory.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/NeuromatchAcademy/course-content/blob/main/projects/theory/RNN_working_memory.ipynb?flush_cache=true) |

## Motor RNN

We built on [Feulner & Clopath, Plos Computational Biology, 2021](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008621) to propose this project. Here we explore how RNN representation dynamics is linked with connectivity structure and task complexity.

|   | Run | View |
| - | --- | ---- |
| Motor RNN | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/NeuromatchAcademy/course-content/blob/main/projects/theory/motor_RNNs.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/NeuromatchAcademy/course-content/blob/main/projects/theory/motor_RNNs.ipynb) |


## Databases of models
​
Here is a list of cool databases you might want to use to look for existing models, computational analyses / data processing tools and data. 
​
| Name                                                  | Model? | Analyses? | Data? | Description                                                  |
| ----------------------------------------------------- | ------ | --------- | ----- | ------------------------------------------------------------ |
| [BioModels](https://www.ebi.ac.uk/biomodels/)         | :+1:   |           |       | **BioModels** is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. |
| [ModelDB](https://senselab.med.yale.edu/modeldb/)     | :+1:   |           |       | **ModelDB** provides an accessible location for storing and efficiently retrieving computational neuroscience models. A ModelDB entry contains a model's source code, concise description, and a citation of the article that published it. |
| [Open Source Brain](https://www.opensourcebrain.org/) | :+1:   |           |       | **Open Source Brain** is a resource for sharing and collaboratively developing computational models of neural systems. |
| [CRCNS](http://crcns.org/)                            | :+1:   | :+1:      | :+1:  | **CRCNS Data sharing website** is a marketplace and discussion forum for sharing tools and data in neuroscience |
| [EEGbase](http://eegdatabase.kiv.zcu.cz/home-page)    |        | :+1:      | :+1:  | **EEGbase** is a system for storage, management, sharing and retrieval of EEG/ERP data, metadata, tools and documents related to electrophysiology. |
| [INCF resources](https://www.incf.org/resources/sbps) | :+1:   | :+1:      | :+1:  | A list of resources endorsed by **INCF**.                    |
| [NITRC](https://www.nitrc.org/)                       | :+1:   | :+1:      | :+1:  | **NeuroImaging Tools & Resources Collaboratory** is an award-winning free web-based resource that offers comprehensive information on an ever expanding scope of neuroinformatics software and data. |
​
​
​
## Additional resources
​
| Name                                                         | Description                                                  |
| ------------------------------------------------------------ | ------------------------------------------------------------ |
| [figshare](https://figshare.com/)                            | A database of everything research related that's openly shared |
| [Google Dataset search](https://datasetsearch.research.google.com/) | Lets you do a Google search specifically to find datasets    |
| [NeuroVault](https://neurovault.org/)                        | A public repository of unthresholded statistical maps, parcellations, and atlases of the brain. (MRI and PET) |
| [KnowledgeSpace](https://knowledge-space.org/)               | A globally-used, community-based, data-driven encyclopedia for neuroscience that links brain research concepts to data, models, and the literature that support them. |