American Academy for Biomedical Informatics
AABI

American Academy for Biomedical Informatics

4 Days Hands-on Training, January 10-13, 2017

Training in Advanced Transcriptomics (RNASeq) Analysis

@ National Institutes of Health, Bethesda, MD 20892, USA. Earn 2.8 CEU's from FAES@NIH

nih national institutes of healthfaes at nih

Tools/Skill Taught

  • Differential expression analysis : Tuxedo tools Vs Trinity tools
  • Fusion gene analysis : Tophat-Fusion
  • RNA-Seq SNP detection : GATK
  • Allele specific expression : WASP
  • Circular RNA identification : circexplorer
  • Alternative polyadenylation : DaPars
  • Viral integration : VirusFinder
  • Network analysis : Cytoscape



  • 3 Days Hands-on Training, January 17-19, 2017

    Cloud Computing for Biomedical Researchers

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 2.1 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skills Taught

  • Cloud platform: Amazon Web Services (AWS)
  • Cloud platform: Google Cloud Platform
  • Cloud platform: Azure - Microsoft Cloud Platform
  • Computing: AWS Elastic Cloud Compute (EC2)
  • Computing: Secure Shell, Secure File Transfer (SSH/SFTP)
  • Computing: AWS Identity and Access Management(IAM)
  • Computing: AWS GPU, CPU, Cluster
  • Standards: GovCloud
  • Pricing: On-demand, spot, reserved
  • Storage: AWS Simple Storage Service (S3)
  • Storage: AWS Elastic Block Store (EBS)
  • Storage: AWS Volumens, Snapshots, Amazon Machine Images
  • BigData: Hadoop, MapReduce, DynamoDB
  • Monitoring: CloudWatch



  • 4 Days Hands-on Training, February 7-10, 2017

    Training in Computational Drug Design and Discovery

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 2.8 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skill Taught

  • Ligand preparation : OpenBabel
  • Target preparation: Chimera
  • Databases: ZINC, PubChem, ChemSpider, ChEMBL, DrugBank, Binding DB
  • Docking: AutoDockTools
  • Visualization: Chimera, PyMOL
  • Structure based virtual screening: AutoDock, Dock
  • Ligand drawing & visualization : Chemdraw, Chemsketch
  • Compound library : ChemT (or DRUGSTER or FSees)
  • Descriptors : Mold2
  • QSAR : Open3DQSAR (or TEST or Coral)
  • Pharmacophore exploration : Open3DQSAR (or DRUGON or pharmacophore)
  • Ligand alignment : LIGSIFT
  • Ligand based virtual screening: LIGSIFT (or MOLA or lisica)
  • ADMET, Toxicity estimation : Toxtree (or DataWarrior)



  • 4 Days Hands-on Training, February 21-24, 2017

    Hands-on Training in Metagenomics Data Analysis

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 2.8 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skill Taught

  • Processing and Analysis : mothur, FLASh
  • Analysis : Permanova, ANOSIM
  • Marker analysis : LEfSe, QIIME
  • Functional analysis : PICRUSt, bioBakery
  • Metagenomics analysis : A5miseq
  • Contig annotation : MEGAN
  • Advanced visualizations : phyloseq
  • Network analysis : Cytoscape



  • 4 Days Hands-on Training, March 7-10, 2017

    Training in Molecular Modeling and Molecular Dynamics

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 2.8 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skill Taught

  • Ab initio protein structure modeling: QUARK / Rosetta
  • Remote homology detection: HHpred
  • Fragment-based protein structure modeling: Phyre2
  • Homology-based protein structure modeling: I-TASSER, MODELLER
  • Protein structure quality analysis: PROCHECK, WHAT_IF, Verify3D, PDB-REDO
  • Protein structure refinement: ModRefiner, ModLoop, Ramachandran plot
  • Macromolecular visualization: VMD, USCF Chimera
  • Molecular dynamics: NAMD



  • 3 Days Hands-on Training, March 22-24, 2017

    Hands-on Training in Creating Plots, Graphs and Maps using R

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 3.5 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skill Taught

  • Heat maps, Scatterplots, Regression lines
  • Density plots, Scatter plots with grouping, Bar graphs
  • Jitter plots, Line graphs, Histograms
  • Bubble charts, Pie charts, Time series
  • Box plots, Violin plots, 2D plots, 3D plots
  • Matrix/panel plots, Tree plots, Contour plots
  • Ternary plots, Chord graphs, Candlestick charts
  • Maps with bubbles, scatters, lines, choropleth
  • Word clouds, Dygraphs



  • 4 Days Hands-on Training, April 18-21, 2017

    Training in Data Integration, Analysis and Visualization

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 2.8 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skill Taught

  • Data Cleaning and Preparation: Basic Unix
  • Data Cleaning and Preparation: OpenRefine
  • Network Generation: Cytoscape
  • Data Integration: Cytoscape
  • Enrichment analysis: Cytoscape
  • Pathway analysis: Cytoscape
  • Gene Prioritization: Cytoscape
  • Data Exploration: Cytoscape
  • Data Visualization: Cytoscape
  • Large Graph Analysis: Neo4J



  • 4 Days Hands-on Training, April 25-28, 2017

    Bioinformatics for Beginners

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 2.8 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skill Taught

  • Databases: NCBI-ENTREZ, UniProt, PDB, STRING, Others.
  • Sequence analysis and function predictions: EMBOSS suite & others
  • Local Alignment: EMBOSS-WATER
  • Global Alignment: EMBOSS-NEEDLE
  • Similarity search: NCBI BLAST, PSI-BLAST
  • Multiple sequence alignment: Clustal Omega, MUSCLE, MAFFT
  • Phylogenetics: MrBayes, MEGA, FigTree and Dendroscope
  • Motif finding, analysis: MEME suite
  • Structure prediction, visualization & analysis: PyMOL, Chimera, iTASSER
  • Transcriptome analysis: NCBI GEO, Tuxedo tools, R
  • Enrichment analysis: DAVID
  • Pathway analysis: Cytoscape
  • Programming: R, Perl, Python
  • Platforms: EMBOSS, UGENE, H2O, Galaxy



  • 3 Days Hands-on Training, May 23-26, 2017

    Hands-on Training in Variant Analysis

    @ National Institutes of Health, Bethesda, MD 20892, USA. Earn 3.5 CEU's from FAES@NIH

    nih national institutes of healthfaes at nih

    Tools/Skill Taught

  • NGS Basics, experimental design, data format
  • Data quality control, preprocessing and alignment
  • Germline variant calling
  • Somatic variant calling
  • Variant score recalibration and filtering
  • Variant calling best practices
  • Indels, structural and copy-number variation
  • Cohort and population scale analysis
  • Recombination, linkage, LOH, haplotype, allelic imbalance
  • Variant annotation and association analysis
  • Co-variation, causal variation, network analysis