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¶
Material For Projects¶
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
If you need mass spectrometry data for a project, here are some data resources that you can use to get started.
- Single Metabolomics LC/MS files in mzML Format - Download Link - Dashboard Link
- Entire Metabolomics LC/MS Dataset to Download - Download Link
- Data Independent Dataset Metabolomics LC/MS Dataset - TODO
- Single Spectral Library - MGF Format JSON Format
- All Spectral Libraries - Link
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. Unless otherwise specified, you can sign up on the calendy link that I'll send out and for MWF meetings they will be in person.
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.
The Wang lab helps to organize a UCR Bioinformatics journal club on Wednesday mornings. Everyone in the lab should plan to attend.
How to Use Jupyter Notebook to Commit Code
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.
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
- Template for creating a new Jupyter Notebook
- Template for creating a GNPS Data Reanalysis Notebook
- Template for creating a NextFlow Workflow
- Template for creating a Documentation Website
- Template for creating a Deep Learning
- Template for creating a Dash Webserver
- Template for creating a Flask Webserver
- GNPSData Package to interact with a lot of the resources
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
Here is a list of fellowships for propsective PhD Students, PhD Students, and Postdocs - link
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.
- Database Search
- Significance Estimation
- Target Decoy
- Spectrum Prediction
- Library Search
- Library Building
- DIA Deconvolution
- Protein Inference
- Network Annotation Propogation
- Fingerprint Prediction
- Universal Spectrum Identifiers
- MS2 Motifs
- Feature Finding
- In Silico Fragmentation
- 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