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Wang Lab Resources

Here are a set of resources to help streamline research.

Internal Lab Documentation

There are very specific internal lab documents on how to set up your own machines specifically for the kind of research we do, all that documentation can be found here

Skills for the Lab Research

Link to Lab Skills Research

Material For Projects

Project Template

If you are starting a new project in the lab, I'd recommend to use this lab template - Google Docs Link

Paper Writing Outline

If you are starting to write a new manuscript, I've tried to make it a bit easier - Google Docs Link

Data Resources

If you need mass spectrometry data for a project, here are some data resources that you can use to get started.

  1. Single Metabolomics LC/MS files in mzML Format - Download Link - Dashboard Link
  2. Entire Metabolomics LC/MS Dataset to Download - Download Link
  3. Data Independent Dataset Metabolomics LC/MS Dataset - TODO
  4. Single Spectral Library - MGF Format JSON Format
  5. All Spectral Libraries - Link

Lab Meetings

Group Meetings

As a lab, we will meet once a week with everyone (generally on Wednesdays), so that we can coordinate on any issues and get to know what each person is working on. This will also help to share ideas and discuss any new or old papers that may have relevance for our research.

One on One Meetings

We will have one on one meetings at a minimum weekly. Meetings will be scheduled to be recurring and updated every quarter to reflect changes in schedule.

To prepare you for how to organize this meeting, this document will help you organize your thoughts on progress since our last meeting. Please read through before every meeting so that we can best direct the meeting. link.

Journal Club

The Wang lab helps to organize a UCR Bioinformatics journal club on Wednesday mornings. Everyone in the lab should plan to attend.

Technical Resources

How to Use Jupyter Notebook to Commit Code

Lab Terminology

This will explain what specific names mean within the context of research in our lab. This will include data types, column headers, and other things in mass spectrometry. See the terminology page here.

Coding Resources

This page will give a few code snippets for the most common operations you might want to do in data processing of visualization. Link

Here are some code templates that might help you get started on some projects

  1. Template for creating a new Jupyter Notebook
  2. Template for creating a GNPS Data Reanalysis Notebook
  3. Template for creating a NextFlow Workflow
  4. Template for creating a Documentation Website
  5. Template for creating a Deep Learning
  6. Template for creating a Dash Webserver
  7. Template for creating a Flask Webserver
  8. GNPSData Package to interact with a lot of the resources

Application Materials

Template For Writing Your Own Recommendation Letter

If you have worked in the lab doing research, use this template to ask Ming for a recommendation letter - link

Funding Resources

Here is a list of fellowships for propsective PhD Students, PhD Students, and Postdocs - link

Literature Resources

If you are in the lab, please familiarize yourself with some of these key literature in the field that will get you up to speed.


  1. Database Search
  2. Significance Estimation
  3. Target Decoy
  4. Spectrum Prediction
  5. Clustering
  6. SLGF
  7. Library Search
  8. Library Building
  9. DIA Deconvolution
  10. Protein Inference


  1. GNPS
  2. Network Annotation Propogation
  3. Fingerprint Prediction
  4. Universal Spectrum Identifiers
  5. MASST
  6. ReDU
  7. MS2 Motifs
  8. Feature Finding
  9. In Silico Fragmentation
  10. Machine Learning Fragmentation

Paper Review Template

If you need to write a peer review for a paper, here is a template to get you started - Google Docs Link

Last update: June 20, 2024 22:17:27