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Mark2Cure

Mark2Cure is a web-based, concept recognition, relationship extraction and validation tool for annotating text. It is intended to be a fun and exploratory way to help biomedical research, but can readily be extended to other disciplines of study where publication rates far exceed a researcher's ability to consume and incorporate knowledge from the literature.

Scientific communication is broken.

Progress in biomedical science is all about incrementally building off of the work of others. Currently, it takes far too long for one scientist's work to reach all the other scientists that would benefit. Mark2Cure will make scientific communication more efficient for everyone, leading to faster discoveries and cures for disease.

To be successful, we need your help. Mark2Cure works by directly involving crowds of people just like you.

Please note that as of 3/28/2016 Mark2Cure will be officially hosted on Github instead of Bitbucket. Issues prior to this date were imported using a script, so read carefully or ask for clarification.

Citizen Scientist Volunteers:

If you are interested in volunteering as a Mark2Curator to read documents and help expedite our annotation process, please go to Mark2Cure.org. The information here is primarily for those with computer science, bioinformatics, and/or programming backgrounds who wish to assist with, develop, or build upon the code. If you stumbled upon this accidentally, we sincerely thank you for your interest in Mark2Cure and ask you to join us at Mark2Cure.org instead.

Developers:

Mark2Cure is open-source and welcomes community contributions! Our issue tracker will soon be updated with issues which are readily "up for grabs" and will be marked as quick fix and/or help wanted.

To work on an issue in our issue tracker, please comment on the issue and provide the following information in your comment:

  1. Your intention to address the issue
  2. A rough time line from completion

That's it! We will assign it to you if it makes sense.

While we will always try to be responsive, our team is very small. We ask for your patience if we do not accept a pull request immediately. Our workloads fluctuate, which translates to inconsistent response times on these matters.

Please know that we are very thankful for your help and desire to contribute to this project.

Setup

Server Dependencies

  • sudo apt-get update
  • sudo apt-get upgrade
  • sudo apt-get install build-essential python python-dev python-pip python-virtualenv libmysqlclient-dev git-core nginx supervisor rabbitmq-server graphviz libgraphviz-dev pkg-config libncurses5-dev

Project Setup

  • Make the python virtual environment and activate it

  • virtualenv mark2cure-venv

  • . /var/www/virtualenvs/mark2cure-venv/bin/activate

  • Make the project folder and download the repo

  • sudo adduser deploy

  • sudo /home/deploy/webapps

  • cd /home/deploy/webapps/

  • git clone https://USER@bitbucket.org/sulab/mark2cure.git && cd mark2cure

  • Install all the python related dependencies

  • sudo /opt/mark2cure-venv/bin/pip install -r requirements.txt

Database Migrations

  • sudo /opt/mark2cure-venv/bin/python manage.py schemamigration APP --auto CHANGE_MESSAGE
  • sudo /opt/mark2cure-venv/bin/python manage.py migrate APP

Control

  • . /opt/mark2cure-venv/bin/activate

  • cd webapps/mark2cure/ && git pull origin HEAD

  • sudo supervisorctl restart mark2cure

  • python /opt/python/current/app/manage.py celeryd -v 2 -E -l INFO

  • python /opt/python/current/app/manage.py celerybeat

  • sudo chmod a+x /bin/gunicorn_start

Utils

  • Flow diagram of the database relationships
  • python manage.py graph_models -a -o myapp_models.png

Notes

Mark2Cure detailed installation instructions for developers

These are instructions, tips, and tricks for how to install mark2cure for developers with more detail than above, assuming you might be unfamiliar with much of this technology. Please feel free to let us know if anything is unclear.

Below is the terminal history for installation of mark2cure in a “clean” brand new Macbook Pro. You will likely have a computer that has already been used for development, so you may run into different issues, but hopefully none.

First thing! You will need pip (you probably already have this). pip is important because it is compatible with virtual environments which we will use to compartmentalize different projects that require different versions of software. Mark2cure has a lot of dependencies.

Install Brew using the long command below. It’s a package manager for Apple comps. “installs the stuff you need that Apple didn’t.”

$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Sudo install a few things. You will need to have virtual environments installed. For more information, see Python Virtual Environments.

$ sudo pip install virtualenv

You will also need the virtual environment wrapper: Virtual Environment Wrapper

$ sudo pip install virtualenvwrapper

Open the /.bash_profile.

$ nano ~/.bash_profile

Add the following two lines to your bash profile:

export WORKON_HOME=$HOME/.virtualenvs

source /usr/local/bin/virtualenvwrapper.sh

Then, "source" the profile.

$ source ~/.bash_profile

Make a new directory where you will house your development version of mark2cure (and other development projects you may have). You could call this something like "repos." Go into this directory.

$ mkdir repos
$ cd repos/

Clone the repository so that you have an exact copy of mark2cure. This would be done in your “repos” folder. No need to make a folder called “mark2cure” because “git clone” will do this for you. If you want to develop, then you would make a branch later (see git documentation).

$ git clone https://your_user_name@bitbucket.org/sulab/mark2cure.git

cd into the newly created folder called mark2cure, and make a virtual environment called “mark2cure."

$ mkvirtualenv mark2cure

You want to activate the virtual environment.

$ workon mark2cure

There are two folders called mark2cure. One is a higher level folder, but you should "cd" into the lower level to install the requirements file. The requirements file is just a list of software programs that mark2cure (or any program with a requirements.txt file) is dependent on.

$ cd mark2cure/
$ pip install -r requirements.txt

Databases are needed in mark2cure to save and recall all of the useful annotations provided by the Mark2Curators.

Make sure you download MySQL Sequel Pro and obtain a copy of the MySQL "framework" mark2cure database. See Max or Jennifer for this.

$ brew install mysql
$ ln -sfv /usr/local/opt/mysql/*.plist ~/Library/LaunchAgents
$ launchctl load ~/Library/LaunchAgents/homebrew.mxcl.mysql.plist

If you have issues with graphviz and pygraphviz, you can remove them from the requirements.txt file (for now). Other dependencies probably should not be tampered with.

$ cd repos/
$ cd mark2cure/
$ pip install -r requirements.txt

Make new directory called “env_vars”

$ mk_dir env_vars
$ mkdir env_vars
$ cd env_vars/
$ touch development.sh
$ nano development.sh

Inside the development.sh file will live some special information. Please see Max or Jennifer for the file contents.

$ cd mark2cure/
$ source env_vars/development.sh
$ echo $MARK2CURE_DATABASE_URL

You will also need the NLTK database Natural Language Tool Kit. Download NLTK using the following commands and follow download instructions in the popup window; download everything.

$ sudo pip install -U nltk
$ python

Running the Python shell will allow you test that the download was successful:

import nltk

Run the unit tests:

$ python manage.py test

At this point, all tests should be passing. After all the tests work correctly, then you can run the server.

$ python manage.py runserver_plus

You should now have a local development version of Mark2Cure!

Install “tree” so that you can see a data tree of your current working directory to see the Mark2Cure application layout.

$ brew install tree

mark2cure development details

When doing manual testing of the mark2cure application (i.e., using the website, and not using the command python manage.py test), you will go to the development server site(Django development server), and you will realize that you cannot get past the "log in" page. To fix this, you can run these commands to force the development server to let you get to the "test_user" account.

From terminal, use python manage.py shell_plus and run the following Python commands:

User.objects.create_user('test_user', password='password')


This does not solve the issue of a "simulated database with real content for testing"... more to come.

Misc. Information about the project (to be expanded):

Ypet is a Javascript library built in Marionette.js to rapidly annotate paragraphs of text on websites. YPet was developed to rapidly annotate bio-medical literature for mark2cure at The Su Lab by Max Nanis.

Troubleshooting:

You will need to create an account to Sentry to log in and monitor error codes and issues with both development and production versions of mark2cure.

When running $ python manage.py runserver_plus" did you get this error?:

Secret value 'SENTRY_PUBLIC_KEY' is not set

This indicates that you must do the following:

$ echo $MARK2CURE_SENTRY_PUBLIC_KEY

Oh no, nothing is there, so you must "source" the development file:

$ source env_vars/development.sh
$ echo $MARK2CURE_SENTRY_PUBLIC_KEY

There, now you should see the key output and can run $ python manage.py runserver_plus" successfully for testing on the local server.

The Scripps Research Institute

Mark2Cure is distributed under the MIT License