BIOINFORMATICS & MODELING CORE | CAIPP

ABRF Policy for Authorship and Core Acknowledgment

The CAIPP Bioinformatics and Modeling Core contributions should be recognized on publications.

1. Co-authorship is requested if the Core made substantial contributions and was essential to the success of the project. Significant contributions include but are not limited to development of pipelines, analysis and interpretation of data, critical input, original ideas, experimental design, and advancing the biological question being addressed in the publication.
2. In cases of routine analysis, the contributions of the CAIPP Modeling Core and should be included in the acknowledgement section of the publication.
3. Manuscripts using services of the CAIPP Modeling Core should cite the COBRE Grant Award

Example

We would like to acknowledge the services offered by the Center of Applied Immunology and Pathological Processes Bioinformatics and Modeling Core supported by the NIH/NIGMS CoBRE Award, P20 GM134974 (PI, Andrew Yurochko).

RRID:SCR_024779

The Bioinformatics and Modeling Core supports the following analysis:

• DNA-seq
• GATK variant calling analyses
• ATAC-seq
• ChIP-seq/Cut-&-Run-seq
• 3C and HiC-seq
• Methyl-seq
• RNA-seq 
• Single-cell RNA-seq
• Spatial RNA-seq
• Small RNA-seq
• Multi-omics integration with mass spec and metabolomics
• AlphaFold Protein Structure Prediction
• Pathway Analysis (ClusterProfiler, EnrichR, LINCS, GeneSet Enrichment Analysis)
• Customized project-specific pipelines and data science, eg. small genome analysis

Please contact us for quotes and pricing information.

The CAIPP Bioinformatics and Modeling Core is equipped with the following:

1. Two Dell Precision Workstations running Windows and Linux operating systems:
   A) Precision 87920 Tower with Intel Xenon Gold 5220R 2.2Ghz, 4.0GHz Turbo, 24 cores, 1TB memory, Nvidia RTX A5000, 25GB GPU, 43-inch monitor
   B) Precision 7920 Tower, Intel Xeon Gold 5220R 2.2 GHz; 4.0GHz Turbo, 24 cores, 512GB memory, Nvidia Quadro RTX5000 16GB, 27-inch monitor
2. MacPro Workstation (2.7GHz 24‑core Intel Xeon W processor, Turbo Boost up to 4.4GHz; 192GB memory; Radeon Pro W5700X with 16GB of GDDR6 memory; 10TB SSD storage, 27-inch monitor)
3. Mac Studio Workstation (Apple M1 with 20-core CPU, 64-core GPU, 32-core neural engine, 128 GB memory, 8TB SSD storage, a 27-inch monitor)
4. iMac with a 24-inch monitor
5. 65-inch LG TV screen for data presentation and visualization