<commit_before># BioTraq

BioTraq enables a simple and flexible tracking of core unit projects.
In addition classical laptop or desktop computers, it is also well usable from mobile devices like tablets and smartphones.

* Admin and user roles for your staff
* Customers will be notified by e-mail when you create a new or update (optionally) an existing project
* Customers can track the project's progress
* The creation of projects is accelerated by a simple templating system:
    - Use a template
    - Customize the provided project and project-steps
    - Create the new Project and save the customized template under a new name
* Ad hoc deviations from the predefined templates are possible.
* Keep track of your old projects with the archive page
 
## Run in demo mode (with default config and without e-mail notification)

For a quick demo of BioTraq switch to the directory where you downloaded the BioTraq jar file and the exemplary ```keystore.jks```. 

```
$ cd biotraq
$ ls
biotraq.jar keystore.jks 
...
```
The run BioTraq as follows to create an initial configuration file and an initial database.
```
$ java -jar biotraq.jar init
```
The files ```biotraq.conf``` and ```biotraq.db``` should have been created.
```<commit_msg>Adds file links to README.<commit_after># BioTraq

BioTraq enables a simple and flexible tracking of core unit projects.
In addition classical laptop or desktop computers, it is also well usable from mobile devices like tablets and smartphones.

* Admin and user roles for your staff
* Customers will be notified by e-mail when you create a new or update (optionally) an existing project
* Customers can track the project's progress
* The creation of projects is accelerated by a simple templating system:
    - Use a template
    - Customize the provided project and project-steps
    - Create the new Project and save the customized template under a new name
* Ad hoc deviations from the predefined templates are possible.
* Keep track of your old projects with the archive page
 
## Run in demo mode (with default config and without e-mail notification)

For a quick demo of BioTraq switch to the directory where you downloaded the [BioTraq jar file](https://github.com/sysbio-bioinf/BioTraq/releases/download/v1.3.1/biotraq-1.3.1.jar) and the exemplary [keystore.jks](keystore.jks?raw=true). 

```
$ cd biotraq
$ ls
biotraq.jar keystore.jks 
...
```
The run BioTraq as follows to create an initial configuration file and an initial database.
```
$ java -jar biotraq.jar init
```
The files ```biotraq.conf``` and ```biotraq.db``` should have been created.
```
{'fraction_non_alphanumeric': 0.06794625719769674, 'fraction_numerical': 0.0023032629558541267, 'mean_word_length': 4.201596806387226, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 1, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 3, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3413918', 'n_tokens_mistral': 739, 'n_tokens_neox': 684, 'n_words': 362}