Gladstone Bioinformatics provides data analysis, programming, and statistics consulting services to the research community.

Our services are open to all researchers. We are located at UCSF Mission Bay, in San Francisco.

For an example of output from one of our analysis pipelines, you can view this PDF of the figures and files generated during an RNA-seq analysis project.

Our list of publications is also available on our research page.

Get started:

Services are open to all researchers.

It's just one step to get started: email us at bioinformatics@gladstone.ucsf.edu with a brief description of your project. We should be able to help with nearly any statistics or bioinformatics request—and in the unlikely instance that we can't, we might know of another group that can.

For billing: if you are a UCSF or Gladstone employee, you probably have an iLab / "Agilent CrossLab" login (you can sign up for a new account at https://gladstone.corefacilities.org/account/signup/34/ ).

Once you have an Agilent CrossLab / iLab account:

•   Go to the Bioinformatics Core: https://my.ilabsolutions.com/sc/2998/bioinformatics-core

•   On that page, click the "REQUEST SERVICES" tab near the top of the site and click the "request service" button on the right side.

Let us know if you run into any problems with this process—the web site can be complicated.

 

Specific services, with costs & time estimates:

  • •  Small-scale consulting projects are billed at an hourly rate.
  • •  We also work on long-term projects. These are often paid as "percent effort" on a grant.
  • •  See below for various examples.

 

Experimental Design & Power Analysis Consultation

  • •  Typical cost: Free–$450
  • •  Typical turnaround time: 1-3 business days
  • •  It can be helpful to consult with us for initial experimental design before running a project. UCSF-affiliated researchers may request a free consultation via CTSI (click [here for UCSF-affiliated researchers] to schedule a free consultation).
  • •  Power analysis (selecting and justifying the appropriate "N" of replicates for your project) is often required for grant applications, and generally takes around 3 hours.

 

RNA-seq, ChIP-seq, ATAC-seq (and other sequence-analysis)

  • •  Typical cost: $1200–$2400
  • •  Typical turnaround time: 5-10 business days
  • •  Details available at this 10-page PDF: http://gb.ucsf.edu/bio/public/Gladstone-Bioinformatics-RNA-seq-workflow-1.6.pdf
  • •  End-to-end complete analysis involves sample QC, alignment, differential expression analysis, generation of a number of figures (described in the PDF above), and hosting of UCSC-compatible Genome Browser tracks.

 

Statistics consulting

  • •  Typical cost: $200–$1000
  • •  Typical turnaround time: 5–15 business days
  • •  If you run into issues dealing with a complex experimental design, or with any statistical questions that you'd like answered, we should be able to assist you.

 

Variant calling

  • •  Typical cost: $1400–$3000
  • •  Typical turnaround time: 10 business days
  • •  We can call variants from your input data and provide VCF file output. Normally, we use the GATK pipeline for this.

 

Data normalization across multiple projects / labs

  • •  Typical cost: $2000–$3000
  • •  Typical turnaround time: 10 business days
  • •  It can be very difficult to use public datasets, or even datasets from two different labs at the same institution, due to lab-specific confounding effects. We use RUVSeq to try to remove the confounding effects and leave you with samples that can be compared to each other.
  • •  This is a popular option for comparing your own lab's data to public data from GEO or SRA. It can be difficult to find suitable public data sets, but this can be more cost-effective than running your own samples.

 

General programming

  • •  Typical cost and turnaround time varies with project complexity.
  • •  If you need custom programming (e.g. processing of text files, writing an analysis pipeline for re-use, etc.), please email us a description of your project. Previous projects have been written in Python, Perl, R, Java, and as bash scripts.

 

Custom Figures for publication

  • •  Typical cost: $150–$600.. Depends on figure complexity.
  • •  Typical turnaround time: 1–5 business days
  • •  We can make publication-quality figures from your input data. Just provide your data and a "napkin sketch"-style outline of what you had in mind, and we'll work with you to figure out the specifics.

 

Other services

 

  • •  Gladstone also provides additional services, such as tutorials for learning common software tools (e.g. Microsoft Excel and Adobe Illustrator).
An example Figure

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Or stop by on the second floor in room 229 of the Gladstone building in Mission Bay