Here, I would like to introduce a bit on what BARTweb can do and how it is contributing to genomics research. Feel free to refer to the Slides to get a better view of this web tool.

Why BART?

• BART can be used to analyze Differentially Expressed Genes (DEG)

  Traditional ways of doing downstream analysis on a bunch of differentially expressed genes are Gene Ontology analysis such as DAVID, or Pathway analysis such as KEGG. Both methods lack information in which TFs regulate the genes.

• Conventional TF prediction methods are sequence-based

  The most popular method of TF prediction is to scan motifs, which only values the promoter regions near the Transcription Start Site (TSS). In other word, it left out distal enhancers. Meanwhile, a sequence-based method engenders a problem that multiple factors may share similar motifs, increasing the chance of finding a wrong TF. Furthermore, a motif does not necessarily mean a binding.

That is what our BART and BARTweb can do - to predict functional regulatory TFs when given only a gene list, a ChIP-seq genomic binding profile or a genome region set. For more details about BART, please refer to the paper here.

Why BARTweb?

In BART, we leverage a large amount of H3K27ac and TF ChIP-seq public data to compute the cis-regulatory profiles, which occupy tremendous disk space and bring intensive computation load.

To release the burden of biomedical researchers from coding and downloading the datasets, we developed this web interface, named BARTweb, to run users’ jobs on our UVA Research computing cluster. In BARTweb, we have updated more available H3K27ac and TF ChIP-seq datasets (numbers are listed in the table) compared to when BART was released. In the meantime, we have optimized the algorithm to shorten the job execution time. Our new version can help reduce job running time from 1.5 hours to around 5-10 mins.

Table 1: the data size comparison between BART and BARTweb.

We are aiming to collect more up-to-date datasets and updating the information annually.

BARTweb workflow and examples

A simple workflow chart is attached here to intuitively illustrate how BARTweb works.

A sample output of a gene set downregulated upon OCT4 (POU5F1) knocked down in a human embryonic stem cell. More intepretations can be found at the help page of BARTweb.

Please feel free to try it out and I am looking forward to any comments!

Step 1: Choose a Framework

Web development mostly could be divided into front-end, back-end and full-stack. Thanks to those GREAT Open Source contributors, there are lots of frameworks to choose from, such as Django, Flask, RoR. Each has its advantages and disadvantages. Since my project would be quite tiny, I chose Flask as my Web Framework.

From my perspective, Flask would be more tiny and lightweight. For a beginner, if you don’t want to waste too much time on learning how a framework works, then I think Flask would be a good choice.

Step2: Learn Basic Knowledge

Take Flask as an example, the only thing you need to know is:

• How to run an app

  # hello.py
  from flask import Flask
  app = Flask(__name__)
    
  @app.route("/")
  def hello():
      return "Hello World!"
  

  $ FLASK_APP=hello.py flask run
  # "Hello World!" gonna show on localhost:5000
  

• How flask routes

  @app.route('/') # localhost:5000/
  def index():
      return 'Index Page'  
    
  @app.route('/hello') # localhost:5000/hello
  def hello():
      return 'Hello, World'
  

• How flask uses variables through URL

  @app.route('/user/<username>') # localhost:5000/user/<username>
  def show_user_profile(username):
      # show the user profile for that user
      return 'User %s' % username
  

  Note: URL is used for the website, not equivalent to a file path. If you need URL variables to generate a file path, do it inside the function by using the parameters passed by the URL.

  Here is a small example on passing URL to download file. I am not sure if there is a better way, but it works.

  from flask import send_from_directory
    
  # URL: /download/123___a.txt
  @app.route('/download/<userkey_filename>')
  def download_file(userkey_filename):
      user_key, filename = userkey_filename.split('___')  # user_key: 123, filename: a.txt
      download_path = os.path.join(user_key, 'download')
      return send_from_directory(download_path, filename)
  

  In this case, it does not matter what name is your function, since I do not call it from other part. What I do is to bind the URL with the file path. Then when I pass the result containing both of them to the html, when the URL is clicked, it will directly goes to my file path, and download the file.

  from flask import render_template
    
  @app.route('/result', methods=['GET', 'POST'])
  def show_result():
      results = {'url_file': ['/download/123___a.txt', 'a.txt']}
      return render_template('result.html', results=results) # passing values to html
  

  Therefore, in thise case, href = related to the url, and `` will show file name.

  When the link is clicked, it will trigger the @app.route('/download/<userkey_filename>') to find the file directory, and sent the file from that directory.

• How the project package looks like

  A project should looks alike flask layout, however, since I use file instead of database and I do not focus on those fancy demonstrations, I compress it into this:

  /home/user/Projects/flask-tutorial			
  ├── __init__.py
  ├── frontend.py         # only do things related to frontend
  ├── do_*.py             # do things related to backend logic
  ├── templates/          # html
  │   ├── base.html
  │   └── error.html
  ├──static/              # static files
  │   └── style.css
  ├── db.json             # file storage
  ├── venv/
  ├── setup.py
  └── MANIFEST.in
  

Step3: Use Open Source Templates

Bootstrap is a GREAT template for those who don’t want to spend much time on how to adjust demonstration. You even don’t need to download the package, just use BoostrapCDN and it will access the network resource to retrieve the style.

Pick one of the Boostrap examples, right click View Page Source. Select all, copy, paste it into one of your templates.

Change the local resource

<!-- Bootstrap core CSS -->
<link href="../../dist/css/bootstrap.min.css" rel="stylesheet">

into CDN resource:

<!-- Bootstrap core CSS -->
<link href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.2/css/bootstrap.min.css" rel="stylesheet">

Step4: Start Building Your Own

This is a passage which not only a tutorial, but also a reminder. Skills could be forgot easily without use. I hope when I finish my current project on Find the Transcriptional Binding expectedly before October due to server reasons, I will publish a full link here. Let’s just get it!

Special thanks to Jiaying Lu who taught me these quick web development skills and gave me technical instructions with no reservation.