Bioinformatics How Do I?

How Do I? » Bioinformatics | Cellomics | Genomics | Proteomics


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Whom should I contact?
Most of clients have their data generated from other ICBR facilities, such as Genomics Group or Proteomic Group. In such cases, data will be automatically transferred to our bioinformatics staff if preferred. However, if you have data generated from other sources, please feel free to contact any of our bioinformatics staff as you see appropriate. In general,
  • Dr. Li Liu is responsible for genomic and proteomic analysis.
  • Dr. Jason Li is responsible for microarray analysis.
  • Dr. Fahong Yu is responsibile for transcriptomic and phylogenic analysis.
  • Dr. Yijun Sun is responsible for gene marker identification and advanced algorithms related to pattern recognition.
  • Mr. Aaron Gardner is responsible for platform development, system administration and web design.
Our staff is available for free consultations until the actual analysis starts.
How do I submit input files, and how do I receive results?
We prefer face-to-face communications before / during / after the analysis. Input files and output files are preferably transferred and explained during our face-to-face communications. If such interaction is impossible, we will set up a temporary FTP site for file transfer.
General information on EST assembly project
    How do I start?
  • Ideally, we need PHD files. Alternatively, we can start with FASTA files.
    What is the common protocol?
  • Quality clean
  • Vector and/or linker masking
  • Mitochondrial sequence removal
  • Chloroplast sequence removal
  • rRNA/tRNA removal
  • Other customized contamination sequence cleaning
  • Seed clustering if desired
  • Clustering
  • Assembly
  • Align mRNA to genomic sequences if desired
    What software do we use?
  • Paracel TranscriptAssembler
    What are the deliverables?
  • Assemblies, including seed cluster contigs, seed cluster singlets, cluster contigs, cluster singlets, and singlets
  • EST destinations, i.e., which cluster and contig each EST goes to
  • Clustering statistics, i.e., size and members of each cluster
  • Assembly statistics, i.e., size and contributing ESTs of each contig
  • A work log describing each major step and their status.
General information on microarray analysis projects
    How do I start?
  • If you plan to conduct a microarray study using ICBR facilities, we highly recommend that you meet with our Microarray Lab staff and our bioinformatics staff to discuss your experiment design before you order arrays. If you already have your data, we are able to start the project with any of the following files - TIFF images, feature extraction files, or signal intensity files.
    What are the common analysis protocols?
  • We will customize our general protocols according to your specific experiment design and data set. In general, the analysis protocol includes QA/QC, normalization, statistical analysis (parametric and/or non-parametric), functional analysis (GeneOntology and pathway), and gene marker identification if needed.
    What software do we use?
  • SAS/JMP microarray analysis package
  • ICBR AnalyzeIt Tools
  • Resolver
  • BRB ArrayTools
  • Cluster / TreeView
  • PathwayStudio
    What are the deliverables?
  • Before the analysis starts, you will receive a document describing the proposed analysis methods and procedures, and the rationales
  • A list of genes that are significantly regulated based on statistical criteria and/or fold changes
  • Annotations
  • GeneOntology categories
  • Pathways (if available)
  • Gene markers and their prediction powers (if needed)
  • Any figures and tables for manuscripts
  • After the analysis finishes, or any time in the middle of the analysis if necessary, you will receive a work log file with detailed description of analysis steps, explanation of the rationales, the intermediate files, the final outputs, special notices, etc.
General information on custom microarray design project
General information on proteomic analysis projects
Under development
General information on metagenomic analysis projects
Under development

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