Currently, this website serves as the portal for the NeuroBorder project — an integrated platform for data management, analysis, visualization, and documentation.
At the currect stage, documentation is available in the Blogs menu, and tools can be found under the Tools menu. Additional features will be rolled out soon.
Have an idea? I’d love to hear it — share it with me!
Always start by reading the relevant documentation; if you need further guidance, just let me know and I’ll post a guide.
Please visit Galaxy Blogs to have an overview about Sheng Lab Ubuntu server, NeuroBorder Galaxy analysis platform, NeuroBorder Shiny Web App etc. for data management, analysis, visualization, etc.
Internal links
Below is a list of internal links (i.e., they cannot be visited outside the KIZ network) commonly used within the lab:
Ubuntu server:
172.16.50.209. You should access it via an SSH client (for both data analysis and file transfer) or an SFTP client (for file transfer only). Before connecting via SSH, verify that you have bash login permission.NeuroBorder Shiny Web App: https://172.16.50.209/r-shiny/neuroborder/.
NeuroBorder Galaxy: https://172.16.50.209/galaxy/neuroborder/.
Access RStudio in a web browser: https://172.16.50.209/rstudio/server/.
Archive directory: https://172.16.50.209/archive/. This is used to share some data within laboratory. Any members can upload their data to here.
Database directory: https://172.16.50.209/database/. This is used to share some (biological) data within laboratory. Any members can upload their data to here.
Synology NAS: http://172.16.50.55:5000/.
Below is a list of links for various purposes:
Metascape: https://metascape.org/gp/index.html#/main/step1. You can perform various annotation analyses over a gene set like GO enrichment analysis. It can cluster significantly similar GO terms together when you perform GO enrichment analysis. This is quite useful for picking interesting GO terms from an extensive list of GO terms.
g:Profiler: https://biit.cs.ut.ee/gprofiler/gost. Used for ORA (Over-Representation Analysis) or GSEA (Gene Set Enrichment Analysis) (Recommended).
Enrichr: https://maayanlab.cloud/Enrichr/. The same as g:Profiler.
DAVID: https://davidbioinformatics.nih.gov/. The same as g:Profiler.
GSEA official: https://www.gsea-msigdb.org/gsea/index.jsp.
Comparative Mammalian Brain Collections: https://brains.anatomy.msu.edu/museum/brain/.
WashU Epigenome Browser: https://epigenomegateway.wustl.edu/.
UCSC Genome Browser: https://genome.ucsc.edu/.
Timetree of Life: https://timetree.org/home.
NIH’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative - Cell Census Network (BICCN): https://www.biccn.org/.
Easy use for Windows 10/11: https://www.bilibili.com/opus/904672369138729017/. It provides one of the most convenient ways to disable Windows update for decades.