Camplab Wiki

Meeting schedule

All following meetings take place at the big conference room (E605).

Recurring meetings	Time	Description
Camplab lab meeting	Every Friday 10:00 am - 11:00 am	Lab meeting
CBM seminar	Usually every other Tuesday 3:00 pm - 4:30 pm	Each time two students/post-docs/staffs will talk about their research. Check your email for exact date and time.
Computational meeting (Spira-Lenburg Lab)	Every Wednesday 1:00 pm - 3:00 pm	Useful for getting an idea about what other students are doing and practising your presentation skills. Talk to Marc if you want to go to this meeting.
Single-cell working group meeting	Once a month	Campus-wide seminar. Check email for exact date and time.

Lab meeting

See link for lab meeting schedule (BU email required): https://docs.google.com/spreadsheets/d/1qzpoEEwaj6YNmaUcqKC1CC1_cj0wcP8X6cnwUogQKWQ/edit#gid=0

Email lists

Send an email to Josh be added to these lists

• Camplab: camplab-list@bu.edu
• Single cell working group: cbmsc-list@bu.edu

Slack workspaces

• Camplab: https://camp-lab.slack.com
• Compbiomed: https://compbiomed.slack.com/
• Single Cell Core: https://bucores.slack.com

SCC4 directories

• /restricted/projectnb/camplab. Camplab root directory.
• /restricted/projectnb/camplab/home. Lab members' own workspaces. Create a folder with the same name as your BU username and put your stuff in it.
• /restricted/projectnb/camplab/projects/celda/Datasets/10X. Publicly available 10X datasets.

Running interactive sessions on SCC

• Computational Biomedicine has its own node where interactive jobs can be run. Put the following line in your ~/.bashrc file on SCC: alias cb1="ssh scc-cb1.scc.bu.edu". Then you will be able to type the command cb1 to start an interactive session.
• Alternatively, you can request an interactive session on SCC using qrsh

R Package development tips

• R Packages (Hadley Wickham)
• Coding Style Guide
• Robust and Efficient Code
• Rstudio configuration
• FAQ on package development
• Vim
  • Interactive Vim tutorial
  • Vim cheetsheet (by Allison McKnight)
• Git
  • Git cheetsheet
  • Git mergetool tutorial
• GitHub
  • Hello World
• Object documentation

Useful links:

CBM Bootcamp Videos and Slides

Bootcamp1: Nuts and Bolts of Sequencing

https://echo360.org/media/b5c27b50-965c-4b78-bb1c-7ceb46e16351/public https://www.dropbox.com/s/67tnpire1hcqqpy/20161130_Sequencing_Bootcamp_Session1.pptx?dl=0

Bootcamp2: RNA-seq analysis

https://echo360.org/media/ff432a03-11a5-4501-adc3-947370c8f17e/public https://www.dropbox.com/s/2jfci3wwtim1k6v/20161207_Sequencing_Bootcamp_Session2.pptx?dl=0

Bootcamp3: DNA-seq / cancer genome analysis

https://echo360.org/media/37f30058-7631-4985-8d0a-1ba9301c78b0/public https://www.dropbox.com/s/n8qse44negjttq4/20161214_Sequencing_Bootcamp_Session3.pptx?dl=0

Single Cell Data Analysis Tutorials:

• Analysis of single cell RNA-seq data: https://scrnaseq-course.cog.sanger.ac.uk/website/index.html
• Orchestrating Single-Cell Analysis with Bioconductor: https://osca.bioconductor.org/
• Introduction to single cell RNA-seq analysis: https://hbctraining.github.io/scRNA-seq/lessons/pseudobulk_DESeq2_scrnaseq.html

Reviews:

Single Cell:

• Papalexi E, Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol. 2018;18(1):35-45.
• Potter SS. Single-cell RNA sequencing for the study of development, physiology and disease. Nat Rev Nephrol. 2018;14(8):479-92.
• Svensson V, Vento-Tormo R, Teichmann SA. Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc. 2018;13(4):599-604.
• Tanay A, Regev A. Scaling single-cell genomics from phenomenology to mechanism. Nature. 2017;541(7637):331-8.
• Luecken MD, Theis FJ. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol Syst Biol. 2019;15(6):e8746. Published 2019 Jun 19.

Research Computing Services Tutorials

The Research Computing Services (RCS) group, part of Boston University Information Services & Technology, offers a series of tutorials on programming, high performance computing, and scientific visualization. These tutorials are free and open to all members of the Boston University community.

• Tutorials Schedule
• Tutorial Slide Sets

Marker gene list

Google sheet containing information about marker genes and their corresponding cell types: https://docs.google.com/spreadsheets/d/1XZ1oAI74ZhCj7gEGgvZUB_ybHF9iFkJGXam6dPTh1gs

Set up network printer

Instructions: https://www.bumc.bu.edu/it/support/printers/install/

The BU tag number for the printer (Ricoh Aficio MP C4502A) is: 920622.

Get an account on the SCC

Ask Josh to add you to the camplab project.

More information: http://www.bu.edu/tech/support/research/system-usage/scc-quickstart/#ACCOUNT

BU ID card access:

Go to 710 Albany St. for card access to the floor.

• https://www.bumc.bu.edu/publicsafety/services/id/
• https://www.bu.edu/terriercard/