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BioTech Laboratory Workshops

Providing Premier "hands-on" Laboratory Training at the NIH

FAES @ NIH offers an expansive catalog of introductory and post-graduate level bench scientist developed curricula to train in biotechnology laboratory techniques.  To date, we have trained 16,000+ scientists and our classes are team taught by National Institutes of Health active researchers, experts in academia, and industry leaders.

 

Visit the BioTech Calendar to register for our upcoming workshops.

Training Rates for 2017 Calendar Year

Length of Classes General Rates Academia, Gov’t, Military NIH Community NIH Trainees
2-Day Classes $995 $795 $695 $395
3-Day Classes $1,095 $895 $795 $495
4-Day Classes $1,195 $995 $895 $595
5-Day Classes $1,295 $1,095 $995 $695

Click on a Workshop Title to learn more about a class.

BioTech 1 - BioTechnology Techniques This lecture and laboratory course will provide the theoretical basis and the hands-on experience needed for the understanding and execution of those laboratory procedures which are widely used in biotechnology, molecular genetics, immunology, and biochemistry. While the subject matter will be discussed in the context of broadly stated research objectives, the emphasis will be on the techniques rather than on specific applications and strategies. Thus, the participants will acquire skill in the use of "generic" methods, and through an understanding of such methods, improve their effectiveness as workers in a contemporary research laboratory.

Lecture and Laboratory Topics:  Recombinant DNA, Separation, and Monoclonal Antibody Procedures: these will include Gel Electrophoresis (acrylamide and agarose); Column Chromatography; Immunocytochemistry; ELISA; Spectrophotometry (quantitation; enzyme kinetics); Nucleic Acid Purification and Molecular Weight Determinations; Cell Separation Methods; Protein Separation and Quantitation; Liquid Scintillation (double label) Counting; Autoradiography (cellular and gross); and Restriction Enzyme Mapping; Gene Expression; Oligonucleotide Synthesis.

 BioTech 2 - Recombinant DNA Methodology

This lecture and laboratory course is designed to provide the novice with anintroduction to the molecular biology of nucleic acids. An approach emphasizing both principles and methodology provides the scientist with the essential fundamentals needed for gene cloning and for an appreciation of the strategies of recombinant DNA technology as well as other molecular techniques.

Lecture Topics:
Introduction to Nucleic Acids and Molecular Cloning; Isolation and Purification of Nucleic Acids; Restriction Enzymes and Restriction Mapping; Other Pertinent Enzymes; Analysis of DNA and RNA Sequences; Northern and Southern Blot Analysis; Construction of Nucleic Acid Probes; Mapping; cDNA Synthesis Part I: cDNA Synthesis; Construction of cDNA Libraries; PCR-Derived cDNA Libraries; Enzymology; cDNA Synthesis Part II: Screening for Differentially Expressed Genes;  Microarrays;  Differential Display; Subtraction Hybridization; Subtraction Cloning; The Polymerase Chain Reaction Part I: Principles, Theory, Optimaization; Contamination; The Polymerase Chain Reaction (PCR), Part II – PCR Variations: In Situ PCR, Mutagenesis PCR, Real Time PCR, Digital PCR, PCR Arrays, PCR SSCP,  PCR Nested, and Muliplex PCR; DNA nad RNA Sequencing; Bioinformatics; Expression of Cloned Sequences and Their Assays; Epigenetics: Principles and Applications.  

Laboratory Topics:
Laboratory Session I: 
Extraction of High Molecular Weight Genomic DNA from Mammalian Cells;
Restriction Enzyme Digestion of Recombinant Plasmid; Gel Electrophoresis:
Separation of Restriction Digestion Products on Agarose Gel Purification of
Restriction Fragment: Excise Fragment from Gel; Southern Analysis: Blot DNA toMembrane.

Laboratory Session II
Extraction of Total RNA from Mammalian Cells; RNA Gel
Electrophoresis; Isolation and Purification of DNA from Agarose Gel Slice;
Ligation of Purified DNA Fragment into Vector;

Laboratory Session III
Transformation of Bacteria; Southern Analysis: 3` End-Labeling
of Probe with Biotin; PCR: Amplification of Human SIX 6.

Laboratory Session IV
Extraction of Plasmid DNA from Bacteria; Agarose Gel
Electrophoresis of Plasmid and Chromosomal DNA; Southern Analysis:
Hybridization of Probe to Membrane and Chemiluminescent Detection; C. PCR:Electrophoresis and Analysis

BioTech 4 - Cellular Immunology: Principles and Methods

Course emphasis is placed on understanding the immune system principles and the core immunology research methods. Particular focus will be placed on the cellular elements and their roles in the orchestration of the immune response. Because this field is contributing to novel therapies and is in a high state of flux, due attention will be given to new directions.

Lecture and Laboratory Topics 
Cells of the adaptive immune system and of the innate immune system; special focus on B lymphocytes and T lymphocytes; Interactions between antibodies and antigens; Genes encoding antibodies; Immunological memory and the mechanisms involved in recall responses; The Major Histocompatibility complex (MHC) and how it controls adaptive immune response; Immunological tolerance and how the immune system is kept under control; Immunotherapy; How to generate and produce monoclonal antibodies; Using a flow cytometer for the analysis of cells of the immune system; Immunological assays (T cell proliferation, cytotoxic T lymphocyte cell assays, Western Blotting/Immunostaining, ELISA); The Mucosal Immune System.

Related BioTech Course
BioTech 8:  Immunochemistry and Monoclonal Antibody Production

BioTech 7 - Animal and Human Tissue Culture  

This lecture and laboratory course is structured to provide life scientists who are not experienced in cell culture with an introduction to principles and practices that will facilitate their ability to develop the use of in vitro systems. Additionally, investigators without formal training in tissue culture techniques will find the information and laboratory exercises extremely useful. This workshop is predicated on the application of the most rigorous principles of quality control and will be taught by experienced researchers with extensive years of experience in the field.

Lecture Topics
From Donor to Cell Lines: The in vitro environment: Setting up a Tissue Culture Facility, Equipment, Judicious use of Antibiotics, Mycoplasma Effects and Testing, Good Tissue Culture Practices, Cell Line Authentication and Cross Contamination, Nutrients and Plating Surfaces, Experimental Designs; Sources for Tissue Culture; Cell lines and Primary Culture, Adult, Embryonic, and Induced Pluripotent Stem Cell Lines, Tissue Culture from Different Species, Normal, Immortalized, Tumor Cell Lines, 3-dimensional Platforms; Cell Engineering, Transient and Permanent Transfections, Expression Constructs, Oligonucleotides, Viral Vectors, and Transductions; Properties of Normal and Transformed Cell, Finite Life Span, Low Density, Clonal Growth, Mutagenesis: Cell Repositories, ATCC, Rutgers, and Coriell Insitute for Medical Research; Toxicity Testing in the 21st Century, Organs on a Chip, and Other Applications of in vitro Techniques. 

Laboratory Topics 
Subculturing Different Cell Lines: Gross Cytology and Cell Counting, Staining; Cell Cycle and Mycoplasma Analysis; Cell Line Authentication; Karyotyping and Chromosome Breaks; Cloning: Cloning by Limit Dilution and Cloning Rings; Plating Efficiency and Colony Forming Assays; Transformed Cells: Growth Patterns,  Growth in Soft Agar and Collagen Gels; Cell Purification by Centrifugation and Cell Surface Antibody; Viability Assays, Fluorescent, Apoptotic, MTT, LDH and ATP Assays; Transfection and Transductions, Reporter Assays, Stem Cell Differentiation

BioTech 8 - Immunochemistry and Monoclonal Antibody Production 

 

The objective of this lecture and laboratory course is to provide investigators with information on chemical approaches to the isolation, purification and characterization of antibodies and antigens. Special emphasis will be given to 
monoclonal antibody formation, assay, and characterization.

Topics
The Immune Response; Immunoglobulin Structure and Diversity; Immunogenetics; Antigenic Determinants; Idiotypic Network; Application of Monoclonal Antibodies; Cell Fusion; Myeloma Cell Lines; Screening for Monoclonal Antibodies (ELISA, Immunofluorescence, RIA); Cloning; Purification and Characterization Approaches; Human Monoclonal Antibody Formation and use; Crystal Structure; Purification of Antibodies from Serum, Ascites, and Culture Supernatant; Analysis of Antibody-Antigen Reactions by Immunoprecipitation and Equilibrium Dialysis; Affinity Determinations; Production of Idiotypic Antibodies, Antibody Fragments, and Novel Antibodies; Peptide Carriers and Antigen Synthesis; Radioreceptor and Crosslinking Assays for Cell Surface Receptors; Immunocytochemistry; Recombinant DNA Approaches.

BioTech 16 - Expression, Detection, and Purification of Recombinant Proteins in Prokaryotic & Eukaryotic Cells

 

This 3 day lecture laboratory course will give the student a good theoretical background and practical experience in expression and purification of recombinant proteins from a variety of expression systems. Furthermore, the course will address new methods to overcome traditional challenges in recombinant protein expression and purification. Finally, students will be introduced to methods to prepare their samples for downstream applications such as immunofluorescence studies.

Lecture and Laboratory Topics 
Introduction to Protein Purification Techniques; Expression of Proteins in 
Prokaryotic and Eukaryotic Cells: Requirements, Advantages and Disadvantages; Prokaryotic Expression Systems: Strains, Tags and Purification Systems; Expression in Insect Cells: Baculovirus and Drosophila Systems; Expression in Mammalian Cells: Detection and Purification (Immunohistochemistry, Reporter Gene Assays, GFP, Tags for Expression/Purification Systems); Generation of Antibodies to Recombinant Proteins: System considerations and Antibody Purification; Expression in Yeast Cells (Pichia).

BioTech 18 - Stem Cells 

The emergence of stem cells as important tools for biomedical research prompts this offering of a 5 day, lecture-lab training course on Stem Cells.

The lectures will cover importance, origin, and fate of diverse stem cells (hematopoietic, muscle, nerve, skin and embryonal) and the factors which control their differentiation. Special emphasis will be on isolation, identification, culture, and use of stem cells and their progeny.

Lecture and Laboratory Topics 
Bone Marrow Stem Cell Plasticity; Hematopoietic Stem Cells; Cell Lines as Models of as Stem Cells; Flow Cytometry and Stem Cell Isolation and Characterization; Murine Embryonic Stem Cells; Mesenchymal Stem Cells; Differentiation of Stem Cells into Bone; Isolation of Cells from Bone Marrow Collection; Histology Marrow vs. Peripheral Blood; Lever Stem Cells; Stem Cells in CNS; Differentiation of Hemotopoietic Cells; Stem Cell Transplantation: Re-engineering the Immune System; Regulatory Perspective Regarding Stem Cells and Gene Therapy.

BioTech 21 - Mitochondrial Molecular Biology and Pathology

The purpose of this five day workshop is to provide a foundation of knowledge to those beginning to investigate mitochondrial function and biogenesis or those simply interested in understanding these essential subcellular organelles.  Participants will learn of the important metabolic reactions occurring within the mitochondria and how nuclear and mitochondrial DNA lesions can result in a wide variety of mitochondrialders. The workshop will include a combination of lectures and hands-on laboratory experiments designed to familiarize the participants with the skills necessary to work with these organelles.

Topics
Structure and Function of Mitochondria; Replication of Mitochondrial DNA and 
Mitochondrial Genetics; Transcription and Processing of Mitochondrial RNA; 
Mitochondrial Protein Synthesis and Import; Molecular Methods for Working with Mitochondria; Mitochondrial Disorders: Molecular Lesions, Phenotypes, Mutation Detection and Approaches to Therapy. Isolation of mammalian mitochondria; Marker enzyme assays; Isolation of mtDNA and RNA; PCR amplification of mtDNA from total cellular DNA; Mutation detection by PCR/RFLP.

BioTech 22 - In Situ Hybridization 

This 4 day course is designed to introduce the participant to molecular hybridization and in situ hybridization techniques.  The application of these techniques to current research questions in genetics and gene expression, molecular pathology, and pathogen detection and identification will be discussed.  Probe application and detection systems will serve as the basis for both RNA and DNA in situ hybridization techniques to be addressed in lecture and laboratory.  This course will be staffed by clinical and basic scientists familiar with the applications of hybridization techniques to the problems of human disease.

Topics
Probe Design, Optimization, and Application at the Chemical and Cytological Levels; Principles of Hybridization; Base Structure, Modification, Stability and Specificity; Hybridization Kinetics; Preparation of Chemical and Cellular Samples; Hybridization Formats: Target Abundance vs. Probe Abundance, Spots/ Blots, Southern and Northern Analysis, Soluble Targets,in situ Hybridization; Radioactive, Biotinylated, DNP, Chemoluminescent and Oligonucleotide Probe Synthesis, Purification and Use; Label and Signal Amplification and Hybridization Accelerators.  DNA in situ hybridization (FISH); Interphase Molecular Cytogenetics; RNA in situ Hybridization; RT-PCR in situ Hybridization; Principles of Karyotyping and Metaphase Chromosome Preparation; Tissue and Specimen Preparation Fixatives, Comparative Genome Hybridization; Spectral Karyotyping; Fluorescence Microscopy; and in situ PCR.

BioTech 23 - Flow Cytometry: Principles and Methods  

This four day lecture/laboratory workshop will cover various applications of flow cytometry in basic research. Selected lecture topics will provide a broad background about the functions of a flow cytometer; choice of fluorochromes; data analysis and presentation; technical protocols for flow cytometric procedures and troubleshooting during data acquisition and analysis.

Lecture and Laboratory Topics 
Basic Setup of Flow Cytometers; Principle of Cell Sorting; Parameters for  Sorting; Alternative Separation Techniques (Including Magnetic Bead Separation MACS); Choice of Fluorochromes Depending on the type of Instrument and Application; Parameters of Analysis, Data Analysis and Interpretation; In-depth Discussion of Examples of Various Flow Cytometric Assays (e.g. Cell Cycle Analysis, Cell Activation, Apoptosis, Immunology, Hematology, Biochemistry with Methodical Protocols); Multi-color Analysis (With Special Emphasis on How to Combine Flurochromes and Fluorescence Compensation); Choosing the Right Controls for Data Analysis (Isotype Controls; FMO controls; Blocking with Antibodies); Hands-on Laboratory with 4- and 8-color staining (BD Accuri and MACSQuant Analyzer); Data Workshop; Hands-on Data Analysis with samples From Cell Cycle Analysis ; Apoptosis; Multi-Color Surface Staining; Proliferation using Bio-Tracers; Software training: Introduction to FlowJo Cytometry Analysis Software.

BioTech 25 - Proteomics: Principles, Methods, and Application to Biomarker Discovery  

This lecture and laboratory course will provide an introduction to proteomics technology. Both principles and advanced methodologies will be discussed with an emphasis on protein identification tools, shotgun sequencing and bioinformatics technologies.

BioTech 26 - PCR Methodology: Principles, Optimization, and Application

Program Description:

From its conception in 1983 to its modern day use in a myriad of clinical and research applications, the Polymerase Chain Reaction (PCR) has revolutionized modern molecular biology. This lecture and laboratory course will focus on the Polymerase Chain Reaction and its applications in basic molecular biology research, genetics, molecular pathology, including cancer and genetic diseases and identification of viral, bacterial and other pathogens.

Lecture and Hands-On Laboratory Training Topics include:

• Conventional PCR

• Dissection and Optimization of the PCR Cycle

• Primer Design and Usage

• DNA Polymerases and PCR Additives

• Reverse Transcription PCR (RT-PCR)

• PCR Variations (Multiplex PCR, Long distance and Nested PCR, and Real time PCR)

• Site-directed Mutagenesis using PCR

BioTech 29 - Laser Capture Microdissection: Methods and Microgenomic

Analysis Laser Microdissection systems allow for the procurement of specific populations of cells from tissue and cytology and live cell culture samples containing heterogeneous populations of cells. The specificity of analyses is therefore much more representative of the disease process being studied. This approach to microdissection ensures that biological molecules, such as RNA and DNA and proteins, remain undamaged during the microdissection process. Downstream molecular analysis of these molecules produces accurate and assured results that have led to over 2,000 peer-reviewed publications by independent researchers.

In this five-day training program, participants learn to prepare tissue specimens for microdissection, then select and acquire homogenous cell populations using the mmi-CellCut, Leica LMD, Arcturus XT, and PALM microdissection systems. Instruction emphasizes operation of these LM systems, appropriate tissue handling and sample preparation for subsequent DNA, RNA or protein analysis, and methods for proper molecular extraction. Lecture and detailed instructions to prepare samples for several downstream molecular analyses are presented.

Lecture and Laboratory Topics 
Overview of Laser Microdissection Technology (History, Theory, Applications); Tissue Sample and Slide preparation; Project set up and QC of microdissected samples, genomic analysis, mRNA analysis including quantitative RT-PCR gene expression analysis and microarrays from microdissected tissue samples, microRNA analysis from microdissected samples, and proteomic analysis from frozen and formalin-fixed, paraffin-embedded microdissected samples using Mass Spec. Special microdissection techniques such as immuno-guided LM and live cells dissections will be also covered.  The lectures also include examples of actual scientific and clinical applications of LM-based studies. The hands on sessions include tissue slide preparation and histology review for LM, and practice on Arcturus XT, PALM, Leica and mmi-CellCut platforms.

BioTech 31 - Vaccine Development and Efficacy

Vaccines are used or developed for a wide range of diseases such as cancer, auto-immune diseases, allergies, and for the prevention of communicable and parasitic diseases. The purpose of this course is to provide an overview of a broad spectrum of vaccine related topics, from the design of vaccines to their delivery with adjuvants and by different delivery systems. The target audience is researchers with various scientific backgrounds and with interest in vaccine research, but also those dealing with regulatory aspects of vaccines who wish to acquire a scientific understanding of vaccines.

Topics
Overview of the Immune System and the Induction of an Immune Response Highlighting Crucial Factors for Vaccinology; Protein and Peptide Vaccines, Viral Vaccines (pox-viruses, adenoviruses), Bacterial Vaccines, Anti-cancer Vaccines; HIV Vaccines and the Unique Challenges this Field Faces; Cutting-edge Vaccines such as DNA Vaccines, Pulsed Dendritic Cells, Nanoparticles; Purpose of Adjuvants, Classes of Adjuvants with in depth Discussion of Adjuvants used in the Clinic, Molecular ("designer") Adjuvants; Immunization Strategies (Regimen, Route of Immunization); Monitoring the Immune Response and Evaluation of Vaccine Efficacy (in vitro Assays such as ELISA, Immunofluorescence Assays, ELISPOT; Flow Cytometry: Protocols such as Intracellular Staining, Tetramer Staining and Phenotyping of Vaccine-reactive Cells will be discussed).

BioTech 33 - Clinical Proteomics and Biomarker Discovery

The emerging field of Clinical Proteomics refers to the application of proteomic technologies to investigate protein expression differences in clinically obtained biological samples. A consequence of these approaches has been the renewed interest in identifying new biomarkers which may useful for the diagnosis of disease or monitoring of patient response to therapy.  Researchers involved in Clinical Proteomics face numerous methodological, analytical, and statistical challenges that need to be addressed in order for successful completion of projects. Additionally, large scale biomarker discovery efforts include the coordination of many different disciplines, such as biochemistry, proteomics and mass spectrometry, clinical chemistry and bioinformatics. In this course, students will be exposed to many of the challenging aspects of biomarker discovery projects, as well as to the numerous analytical platforms that may be employed.

Lecture and Laboratory Topics 
Study Design and Sample Collection/Storage of Clinical Samples; Sample Handling and Preparation (Chromatographic methods to reduce the complexity of the sample, such as ion-exchange chromatography, immunoaffinity depletion); Quality Control and Reproducibility in Measurements; Analytical Tools for the measurement of quantitative difference between clinical samples: 2D gel electrophoresis, including DIGE; MALDI/SELDI-TOF-MS for Serum Protein Profiling, Multiplex Protein/Cytokine Arrays, Differential isotopic labeling, such as ICAT, SILAC Quantitative Data Analysis of 2D and Mass Spec Data Sets; Multivariate Statistical Models; MS Protein Patters vs. Protein Panels for Diagnostic Determination.

Related BioTech Course
BioTech 25:  Proteomics: Principles and Methods

BioTech 34 - Advanced Microarrays

In response to the growing demand to learn how to extract maximum information from the tremendous amount of data generated in a micorarray experiment, FAES is delighted to offer BioTech 34. Beginning with a hybridized array, this four-day course will spend extensive time on optimizing the scanning process and acquiring an informative scan. This data will then be analyzed using GeneSpring software to generate clustering associations. Finally, using microarray and protein interaction data, pathways defining gene interactions will be assessed using Pathway Studio software.

Lecture Topics 
Microarray Scanning and Acquisition of a Good Image; Analysis of Microarray Data by GeneSpring; Managing Microarray Data; Pathway Analysis; TM4: Open-source Software for Advanced Microarray Data Analysis (with a Concentration in TIGR MIDAS and TIGR MeV) Normalize and filter Expression Files. Methods for Clustering Expression Data and Classifying Experimental Samples. Laboratories will Include Scanning a Microarray and Computer-based Experiments Involving Analysis and Manipulation of the Data Using Such Programs as QuantArray, GeneSpring and Pathway Studio.

BioTech 35 - Confocal & Immunofluorescence Microscopy

Through morning classes and afternoon "hands-on" lab sessions, Biotech 35 will focus on two important methods that are used extensively in biomedical research.  Fluorescence microscopy is a useful tool for observing cellular morphology and function that is readily available and relatively simple to learn.  Confocal microscopy has emerged as a powerful and popular extension of fluorescence microscopy, allowing 3-dimensional localization and dynamics of cellular components.  The course is designed as a “boot camp” for those cell biologists just entering the world of confocal microscopy, wishing to utilize the technology to its fullest potential.  Several related, advanced topics are introduced to give participants an overview of future possibilities. 

Classroom Topics
Basic Theory and Practical Aspects of Fluorescence, Immunofluorescence, and Confocal Microscopy; Applications; Specimen Preparation; Spinning Disk Confocal; 2-Photon Excitation; Colocalization of Proteins: Using FRET to show protein-protein interactions; Spectral Unmixing; Live Cell Studies: Translocation and localization of proteins using fluorescent fusion proteins and time lapse imaging; Protein Dynamics Using FRAP (Fluorescence Recovery After Photobleaching), FLIP (Fluorescence Loss In Photobleaching), and PA-GFP (Photo-Activatible Green Fluorescent Protein); Image Processing and Analysis using Fiji. 

Brief classroom introductions without labs: SPIM (Selective Plane Illumination Microscopy, also called Light Sheet Microscopy); 3D Deconvolution; Super-resolution microscopy: SIM (Structured Ilumination Microscopy), STED (STimulated Emission Depletion), PALM (Photo-Activatable Light Microscopy), STORM (STochastical Optical Reconstruction Microscopy), GSD (Ground State Depletion), and PAINT (Point Accumulation for Imaging in Nanoscale Topography).

Laboratory Topics
Rotating in groups of 4 or less, participants will gain hands-on experience with: Sample preparation for Fluorescence/Confocal Microscopy; Acquisition/Optimization of Basic Confocal Scans using Single-point Laser-Scanning Confocal Microscopes, Multiphoton excitation, and Spinning Disk Confocal; Colocalization using multi-color fluorescence imaging; FRET; Spectral Unmixing; Live Cell Imaging: Translocation and localization of proteins using fluorescent fusion proteins and time lapse imaging; Protein Dynamics Using FRAP, FLIP, and PA-GFP; Image Processing and Analysis using Fiji;

Related Bio-Tech Course

BioTech 53: Super Resolution Microscopy- March 15-18, 2016 

BioTech 37 - Real Time and Quantitative PCR

This lecture/laboratory course is intended for those who have a fundamental background in PCR and will address the basic chemistries of real time PCR and the many platforms available.

BioTech 38 - Digital Imaging in Microscopy

This three day lecture and laboratory course will cover the demands of high resolution, color accuracy speed of acquisition, imaging flexibility and low cost all of which are demanded by the field today. Areas that will be addressed will include information related to effective imaging through the microscope as it relates to the camera itself as well as appropriate microscope setup to allow for optimal results in the lab situation.

BioTech 39 - Epigenetics

Sequencing of the human genome was not the endpoint of our goal in understanding human genetics. The chemical modifications to DNA and the chemical interactions involving the manufacture of proteins represents a second level of human genetics termed, epigenetics or epigenomics. Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Research has shown that epigenetic mechanisms provide an additional layer of transcriptional control that regulates how genes are expressed. Epigenetic abnormalities are associated with genetic disorders, cancer, autoimmune diseases, aging and pediatric syndromes, among others.

This course will address the basic principles of epigenetics, the role of epigenetic mechanisms in normal development and human disease, and the development of epigenetically-effective drugs. The objective of the program is to provide a solid foundation of information enabling participants to design experiments when returning to their own research lab. Furthermore to provide a solid background inorder to understand the literature in this rapidly growing field.

Participating instructors are primarily active researchers from neighboring institutes and universities who have been publishing in these areas for several years.

Topics
Lectures cover basic mechanism underlying DNA methylation, histone modification, chromatin organization, noncoding RNA, and gene repression. Moreover, a broad range of topics will be covered in epigenetic research including cancer, development, environmental health, and immunology. The lectures also provide the participant with practical information concerning current techniques in epigenetic research. For example, the application of CHARM, Illumina bead arrays, restriction enzyme analysis, and bisulfate sequencing is discussed in designing experiments and interpreting data.

In the laboratory, attendees gain hands-on experience in techniques including methyl specific PCR, chromatin immunoprecipitation, and global DNA methylation assays.

BioTech 40 - Protein Informatics

This three-day course is the logical next step after genome sequencing or proteomics analyses. The workshop will combine lectures with computer labs to provide an introduction to the bioinformatics resources and methodologies commonly used for protein analyses. Course participants are expected to know the basic biology of proteins, and will leave with the ability to perform detailed analyses of protein sequences and structures.

BioTech 41 - Non-Coding RNAs

Recent advances in whole genome analyses has vastly improved our appreciation of the extensive repertoire of noncoding RNAs, including initially the well-known small microRNAs (miRNAs), and more recently, the long noncoding RNAs (lncRNAs).  While miRNA-target interactions appear to be important in control of post-transciptional levels, lncRNAs appear to have a diverse array of functions including regulation of transcription, mRNA processing and post transcriptional control.  Thus, the current state of the art transcriptional profiling should include technologies for the analyses of protein coding mRNA, miRNAs and lncRNAs.

In this hands-on training workshop, participants will learn the latest information about miRNA and the use of miRNA as a diagnostic tool.

Lecture Topics
Overview of Non-Coding RNAs Biology; Discovery and Expression of Non-Coding RNAs; Post-transcriptional Regulation of Gene Expression Programs; Regulatory miRNA networks of Neoplastic Development in Non-Human Primate Kidneys; Non-Coding RNAs Biogenesis, Function and Analysis; Micro RNAs as Biomarkers of Disease; MicroRNAs and Cancer: From Their Role in Carcinogenesis to their Potential as Biomarkers and Therapeutic Targets in Cancer; Multiplex Amplification-free Technology for microRNA Expression Profiling: Advantages and Challenges; MicroRNA Preparation and Microarray Processing; Microarray Experimental Design and Data Analysis.

Laboratory Topics
Profiling of miRNA Through an Overexpression Model: Reverse Transcription using the miScript II RT Kit; Real-time PCR; Data Analysis.

BioTech 42 - BioTechniques II (formerly Junior Scientist Training Program - JSTP)                                                                                                               Hands-On Laboratory Training for Developing Scientist

This program provides hands-on laboratory training along with web-based lectures geared towards learning techniques in the life sciences.  This intense eight month program is designed to prepare those in the sciences who need to strengthen their laboratory skill set.  Participants acquire knowledge, technical skills and experience neccessary for the next step in their academic or research career. 

Program Description:
The program is held September 21, 2015 through May 23, 2016, encompassing 15 practical laboratory sessions covering the latest relevant techniques in the life sciences. Participants meet weekly on Monday, either online through web-based lectures or in person at the National Institutes of Health for a lab session.  

Topics covered include:
Conventional, Real-Time and Quantitative PCR; Cell Culture; Tissue Culture Techniques: Culturing and Maintaining Mamalian Cell Lines; Cell Counting; Isolation of Nucleic Acids (Genomic and Plasmid DNA & RNA); Immuniassays: ELISA, Western Analysis, Immunofluorescence (IFA); Cloning and bacterial Transformation; Hybridization techniques (Southern and In Situ); Gene Engineering; Gene Expression Analysis: Micro RNAs; Stem Cells; Bioinformatics; and more. 

Ideal Participants:
Life science majors, AA science degree holders, international science students, college graduates who had limited exposure to wet lab training, or those working in the sciences who need to strengthen their laboratory skill set.

Method:
Using FAES's training resources at the NIH, selected students will attend a eight month workshop encompassing 15 hands-on laboratory sessions (75 contact hours) covering the latest relevant laboratory techniques in molecular biology. These selected methods have been identified by NIH scientists and private industry representatives to be techniques that research technicians would implement on a day-to-day basis.

Participants would also be required to view selected lectures online (approximately 30 hours) that are part of the current FAES biotechnology curriculum.  These lectures, which are taught at a graduate level by local researchers, will cover many areas of biotechnology that will introduce and reinforce the subject matter given in the laboratory. NOTE: Participating researchers will be available to serve as mentors for interns who participate in the program.

Results:
Students will gain extensive experience in laboratory techniques that are necessary to excel in the sciences once completed. Upon conclusion of the program, participants would receive six graduate credits; will increase their competitive value for research positions and strengthen their graduate school or internship application if pursuing graduate studies.

BioTech 45 - Bioinformatics Analysis of Next Generation Sequencing Data

This course will introduce students to bioinformatic analysis of next generation sequencing data, particularly for DNA-seq, RNA-seq, CHIP-seq, and epigenomics. The course will be comprised of lectures and hand-on sessions. Lectures will cover background knowledge and survey various software programs. For hand-on sessions, command line tools will be presented and the galaxy web based platform will be used to analyze primary data. Cloud computing, genomic databases, and de novo assembly will be surveyed.

Topics
Overview on Bioinformatics Tools: Galaxy (Pre-processing, Format Conversion, etc.), Databases and Tools, SNP Callers, Cloud; RNA-seq; CHIP-seq; Epigenomics; Cloud Computing; 10k Genomes; Data Visualization; Comparative Genomics and Genome Alignment (biology + software); Tutorial & Laboratory for de novo Assembly; RNA-seq, DNA-sequencing.  

Related BioTech Courses
BioTech 40: Protein Bioinformatics
BioTech 56: RNA-Sequencing 

BioTech 47 - Human Induced Pluripotent Stem Cell (hiPSC) - Differentiation to Neural Lineages 

Induced pluripotent stem cells (iPSC) represent enormous potential in that they are capable of differentiating into virtually any cell type in the human body. Directing this differentiation into specific cell types in a consistent and efficient manner enables researchers to investigate new therapy and screening approaches in patient-derived cells. This 5 day hands-on training workshop will provide participants with the training and knowledge to help the researcher bring iPSC technology to the laboratory. Students will gain practical knowledge for developing new cell lines from different cell types. Lectures will discuss the expression of genes required for inducing pluripotency and methods of making (virus, RNA, plasmid) and maintaining iPS cells. Lectures on conditions needed for differentiating iPSC to neural, epithelial, and hematopoietic lineages will also be discussed. 

The emphasis of the course is on practical information that will help the investigator in the laboratory. Emphasis will be placed on deriving iPSC and differentiation to the neural lineage. Laboratory exercises are intense and will be directed by experts with a working knowledge of the techniques. Labs will cover methods for making iPSC and picking iPSC colonies. In situ analysis of pluripotency on live cells will also be conducted. Laboratory exercise on neural stem cells will include cryopreservation techniques and immunocytochemical analysis of pluripotent marker (Oct4) and neural markers (Sox1, Nestin and Sox2).

Topics 
Overview; Differentiation of Human Pluripotent Stem Cells into NSC; Differentiation Methods; Cell Culture Methods; Introduction to Mouse and Human Induced Pluripotent Stem Cells; Cellular Reprogramming Methodologies; mRNA Reprogramming of Patient Samples; Optimizing mRNA Reprogramming Efficiency; Differentiating IPSC to Retina Pigment Epithelium; Epigenetic Understanding of Pluripotency; Differentiating IPSC from CD34+ cells; Differentiating IPSC to the Hematopoietic Lineage

Differentiation of IPS to Neutrophils; Preparation of Cells From Embryoid Bodies To Study Differentiation; Differentiating IPSC to Neurons; Techniques Used for neural differentiation; Neural Induction and Neural Expansion; NSC Staining for Pluripotent Marker (Oct4) and Neural Markers (Sox1, Nestin and Sox2); Cryopreservation of Neural Stem Cells

Class size will be limited to 16 

BioTech 49 - Making iPSC from Blood 

Recent advances in generating iPSCs now allow for their derivation from blood. This recent advance enables basic and clinical researchers to reprogram a blood cell into an iPSC and then further differentiate into any cell type. This capability allows researchers to develop "disease in a dish" paradigms to investigate disease and therapy mechanisms.

In this one week workshop, participants will learn how to generate iPSC from blood samples using a non-integrating approach. Due to the length of this procedure (iPSC generation ~3-4 weeks etc.) starting material (CD34+ cells or mononuclear cells) will be provided for each investigator and only critical stages will actually be performed during the laboratory portion of the workshop.

In addition to learning how to culture cells and reprogram blood cells into iPSCs, we will also present some of the latest methodologies for directing differentiation of these iPSCs into different lineages (e.g. hepatocytes or cardiomyocytes). Therefore, this course will package together the essential methodology to take a CD34+ cell isolated from blood, reprogram this cell, and then direct differentiation into multiple different lineages.

Lecture Topics
Introduction to Human Induced Pluripotent Stem Cells; Cellular Reprogramming Methodologies, Reprogramming from Blood; Specialized Media and Tools for Isolation and Enrichment of Blood-Derived Cells; Reprogramming using Cytotune Sendai Virus and Episomal Vectors; Differentiating IPSC to MSCs; Differentiating IPSC to RPEs; Overview of Validation Tests for Pluripotency.

Laboratory Topics
Observation of Monday’s cells and Cryopreservation; Maintenance of human iPSCs and Differentiation of iPSCs via Embryoid Bodies or Monolayer Platforms; iPS colony identification from TeSR-E7 Reprogramming Experiments; Making Embryoid Bodies Using Aggrewell; Neural Rosette Identification and Scoring; Reprogramming Using Cytotune Virus; Progression of Colony Formation via Fixed Dishes; Picking of Reprogrammed Colonies; Neon Electroporation, Transfection; Validation Tests for Pluripotency; RT-QPCR Assay for iPSC Characterization.

 

Related BioTech Courses
BioTech 18: Stem Cells
BioTech 47: Human Pluripotent Stem Cells (hiiPSC); Differentiation Neural Lineages
BioTech 54: Making Cardiomyocytes from iPSCs 
BioTech 55: Engineering with CRISPR, TALENs, and ZFNs
 

BioTech 53 - Super Resolution Microscopy: Principles and Methods

Super Resolution Microscopy represents a group of recently developed light microscopic techniques that are able to exceed diffraction-limited resolution (less than 200nm). This course will focus on three types of Super Resolution Microscopy- Structured Illumination Microscopy (SIM), Stochastic Optical Reconstruction Microscopy (STORM), and Stimulated Emission Depletion (STED).  In addition, students will be exposed to cutting-edge super resolution microscopes developed at HHMI Janelia Research Center through the AIC (Advanced Imaging Center).  The AIC will showcase several instruments, including iPALM, lattice light sheet and live-cell TIRF-SIM.  

The course is designed for cell biologists with prior experience in light microscopy who wish to add super resolution microscopy to their research program. Participants will acquire both theoretical understanding of super resolution microscopy and practical experience using state-of-the-art super resolution microscopes.

Lecture Topics 
Introduction to Super Resolution Microscopy; Advances in Super Resolution Microscopy; Theoretical Background of SIM, PALM/dSTORM, and STED Imaging; Advances in Fluorescent Protein and Organic Dye Technology; Applications of Super Resolution Microscopy using SIM and dSTORM; Challenges Associated with Obtaining Good SIM, STORM and STED Images; Potential Artifacts Common to Super Resolution Imaging.

Laboratory Topics
Working in groups of five, participants will rotate through multiple work stations. 
The following work stations are located on NIH campus: 
- Leica gSTED, GE- OMX SIM, Nikon N-STORM, Zeiss Elyra PALM/SIM, Zeiss LSM880-AiryScan, Shroff Lab - Instant SIM, Shroff Lab - Dual View Plane Illumination Microscope.  

Another three stations are located on Janelia Farm campus including iPALM, Lattice light sheet microscope, TIRF-SIM for live cell imaging.  Complimentary transportation will be provided to and from the Janelia Farm campus.  

During the laboratory sessions, the following topics will be covered:
-   Introduction and Feature Highlights of the Instrument
-   Imaging Acquisition Procedures 
-   Sample Preparation Requirements and Recommendations (Dye Choices and Imaging Solutions)
-   Imaging Data Analysis and Presentation
-   Trouble-shoot Common Problems in SIM Imaging
-   Acquisition of 2D and 3D STORM Images

Related BioTech Course
BioTech 35: Confocal & Immunofluorescence Microscopy

BioTech 54 - Making Cardiomyocytes from iPSCs

Often late stage clinical trials are terminated due to cardiotoxicity. There is great need to develop proper screens that are predictive of human clinical response to medications. This course will cover numerous applications using cardiomyocytes. The lectures will cover cardiac development and cardiac diseases which provides the necessary background for this course in appreciating how stem cells can be differentiated from iPSCs and be used to develop disease in a dish models as well as screens to monitor specific cardiac phenotypes such as arrhythmia and cardiac toxicity. Lectures will also cover the methodology to drive differentiation of iPSCs toward cardiac lineages and the development of cardiac reporter lines that will be useful for screening applications. 

The laboratory exercises will include basic handling of cardiomyocytes and then delve into discovery techniques that focus on disease modeling and phenotypic screening for small molecule therapeutics. Lab exercises will 
conclude with providing exposure to transfection techniques as well as assays for proarrhythmia and toxicity.

 

Lecture Topics
Cardiac Development and Disease; iPS and ESC: Methodology for Differentiation of Cardiomyoctyes from ESC and iPSC; iPS and ESC: Overview on Benefits and Limitations of iPSC/ESC-derived Cardiomyocytes; Characterisation and Validation of hESC Derived Cardiomyocytes; High Content Screening for Cardiotoxicity of Anti-Cancer Drugs in hESC Derived Cardiomyocytes; Bioenergetic Modulation of Kinase Inhibitor Cardiotoxicity in hESC Derived Cardiomyocytes; Cardiac angiogenesis and vascular biology; Cardiac Physiology; Cardiac Electrophysiology and Functional Assays; Functional Improvement Following Cell Therapy for Ischemic Myocardium.

Laboratory Topics
Cardiac differentiation from iPSCs ; Basic Handling: Thawing and Plating iPSC-derived Cardiomyoctyes; Discovery Techniques; MEA Demonstration; xCelligance Demonstration; PART I (Transfecting iCell Cardiomyoctyes with one or a Combination of the Following: (a) Fluorescent Protein Marker and Subsequent Analysis via Flow for Transfection Efficiency, Luciferase Reporter, Most Likely CRE-Luciferase and Then Induction and Read-out of the System, (c) siRNA to Knock Down Housekeeping Gene and then Quantify Via Flow or HCl or Knock Down Ion Channels and Provide a Functional Readout); Compound dose response curves; Transfection and reporter assays; Organelle Toxicity; Discovery Techniques PART II: Disease Modeling and Phenotypic Screening for Small Molecule Therapeutics (Hypertrophy With Protein Based HCl Readout and a Phenotypic Screen with 6 Compounds to Look for Amelioration of the Pathology); Reporter Assays; GE Cytell Demonstration: Imaging (GE Lab); Organelle Toxicity; Field Trip to NCATS, Lecture on High Content Screening Methods.

BioTech 55 - Engineering with CRISPR, TALENs, and ZFNs 

Gene engineering provides the ability to manipulate gene expression in a desired cell type. In order to realize the full potential of stem cells, the development of tools to modify targeted genes is paramount. This course will provide an overview of three different engineering platforms including CRISPR, TALENs, and ZFNs.

The first part of the course will cover the general principles of each of these technologies including design and assembly along with the platforms available and different costs associated with each of them. The second part of the course will transition into different applications including engineering in mice, disease modeling, generating iPSC reporter lines, and high throughput approaches.

We will also consider sequencing and quality control considerations for these technologies. Hands on laboratory exercises will accompany lectures to provide training in design, assembly, transfection, and confirmation assays. 

Lecture Topics 
General Principles of Engineering and Disease Models; TALEN-mediated Gene Correction in iPSCs; DNA Repair Mechanisms; Targeted Mutagenesis in Zebrafish using ZFNs and TALENs; CRISPR Engineering in EC Cells and Oocytes for Mouse Model; Targeting Multiple Genes Using CRISPR in Zebrafish; Engineering Mice Using CRISPR/Cas9; Developing Reporter Lines; Panel Discussion to Discuss Current Research Projects; Safe Harbor Gene Targeting of iPSC or Hematopoietic Stem Cells to Correct Monogenic Disorders; Considering Pros and Cons to CRISPR; Engineering Human iPSCs: ZFN, TALEN, CRISPR/Cas9 Advantages and Limitations; Sequencing and Quality Control Consideration.

Laboratory Topics 
Introduction to Genome Editing Technologies; ZFN and CRISPR/Cas Design Considerations; Nucleofection; Gene Knock Out Using Targeted Nucleases; Integration and Detection; Donor DNA Design and Nuclease Compatibility; Exercises for ZFN and CRISPR Design; Bioinformatics for Genome Editing Applications; Development of Genetically Modified Cell Lines Using K562 Cells (will allow attendees to run their own experiments and analyze their own results by the end of this workshop); Engineering iPSCs using CRISPR/Cas9 & HR Targeting Vectors; Introduction to Genome Editing using the CRISPR/Cas9 System; Review gRNA Design Principles, Cloning into SBI’s Cas9 SmartNuclease System, and Best Practices for Use of the CRISPR/Cas9 System for Genome Editing; HR Targeting Vectors for Genome Editing in iPSCs. This Could Cover Basic Knock-out and Gene Tagging Strategies Using SBI’s Existing PrecisionX HR Donors, and Could Also Include Use of Our PiggyBac-HR Vector (PBHR Donor) for Single Base Modifications in Exons, While Incorporating the Cas9/gRNA Constructs Built in the First Section; Generating Stable Isogenic Overexpression & Reporter Lines using the PinPoint Targeted Integration System; Generating PinPoint Platform iPS Cell Lines using the PhiC31 Integrase vs. Safe Harbor-Specific TALEN/HR Donor Combination; Generating Stable Isogenic Overexpression & Reporter Cell Lines using the PinPoint Targeting Integration system.

Class size will be limited to 25

BioTech 56 - RNASeq

RNA-seq or RNA sequencing is a new technology that utilizes the latest in next-generation sequencing approaches to obtain information about the presence/absence as well as the quantity of transcribed RNA (mRNA, rRNA, tRNA, or miRNA). Soon RNA-seq will be transplanting microarrays as the go-to procedure for analyzing the transcriptome of any genome. In this workshop, we will provide hands-on experience with RNA-seq - from the bench to the post-sequencing data acquisition (Illumina NextSeq) and analysis using the latest bioinformatics approaches. With a team of researchers from the NIH, area academic institutions and Illumina, we will cover examples of methodological approaches and applications of RNA-seq analysis to a variety of basic science and clinical biomedical research problems.

Lecture Topics 
An Introduction to NGS and RNA-seq; Basics of RNA Sequencing and Analysis; Introduction to Downstream Analysis; RNA-seq Gene Expression Data Analysis Pipeline: Methods, Tools and Issues; Bioconductor and RNA-seq Data Analysis; Integrating Gene Expression and Pathway Analysis in Developing Early Disease Biomarkers: A Genomic Approach; RNA-seq and CHIP-seq with Galaxy; Basic Downstream Analysis of RNA-seq and CHIP-seq Data with DAVID and IPA; Metaseq: A Python Package for Integrative Genome-wide Analysis; RNa seq Data Analysis in the Context of Biological Networks; RNA-seq of the Small RNAs of the Nucleolus; Transcriptome Profiling of CTLs using RNA-seq.

Laboratory Topics 
Processing of RNA libraries; Load Sequencing Reactions; Recovery of Sequencing Data; Using BaseSpace to Analysis RNA-seq Data; Introduction to Linux, Sed, Awk and Bash Scripting; RNA-seq Analysis with the Tuxedo Package- Command Line

Other topics being considered but not confirmed: Circleator: Flexible Circular Visualization of Genome-associated Data with BioPerl and SVG; BioPerl and SVG 

Related BioTech Courses
BioTech 40: Protein Bioinformatics
BioTech 45: Bioinformatic Analysis of Next Generation Sequencing Data

BioTech 57 - Selected Topics in Cell and Molecular Biology

The goal of this six day lecture/laboratory course is to provide graduate-level instruction on molecular and cellular biosciences.  The course focuses on critical thinking and problem solving, using a collection of approaches and emphasizing how fundamental, highly-significant biological problems are solved.  Focusing on four very distinct areas: stem cells, tissue culture, immunology, and proteomics and informatics, participants will obtain a firm foundation of the theoretical information while enhancing their laboratory aptitude.  

Lecture Topics 
Principles Underlying Stem Cell Biology; Different Types of Adult Stem Cells; Pluriptotent Stem Cells; Neural Stem Cells; Epigenetics and Stem Cells; Cancer Stem Cells; Introduction to Immunology; The Advantages of Tissue Culture Models, Cell Lines (Clonal vs Heterog­enous), Constituents of Tissue Culture Models (Media, Serum etc.); Facilities For Conducting Tissue Culture; Principles and Considerations Concerning the Room, Hood, Microscopes, Centrifuge; Introduction into Proteomics; Bioinformatics; DNA, RNA and Protein Databases.

Laboratory Topics 
Cell Culture Assays For Hematopoietic Stem Cells; Differentiating Pluripotent Embryonic Carcinoma Cells; Immunocytochemistry for Stem Cell Markers; Harvesting embryonic bodies from P19 cultures for immunocytochemis­try; Introduction to Flow Cytometry; Application of Flow Cytometry for the Analysis of Stem Cell Markers; Observation of Embryoid Bodies From P19 Cultures; ELISA and Western Analysis, Cell Cultures, Health, Confluence, Attachment; Methods for Subculture; Cell Counting; Clonal assays; Literature Searches Using PubMed, Searches of NCBI Resources Using Entrez, Protein Sequence Database Searches; Moving Toward the PDB; BLAST, Computational Biology: From Sequence to Structure

Intravital microscopy encompasses various light microscopy-based techniques, such as confocal and two-photon microscopy, which enables imaging and investigating biological events in live multicellular organisms under both physiological and pathological conditioinThis hands-on course will focus on intravital microscopy in rodents and will provide NIH investigators with the opportunity to perform pilot studies in their area of expertise. Participants will be assisted in their experiments by trained personnel and will have the opportunity to use different platforms that will be kindly provided by the major microscope manufacturers. 

The course will start with a one-day symposium featuring lectures from leading experts in the field. The daily schedule will include one hour of introductory lectures followed by intensive hands-on training.

 BioTech 62 - Image Processing and Analysis

Bioimaging studies are rapidly becoming more quantitative due to enhanced imaging technologies, improved analytical and computational tools, as well as increasingly more stringent scientific scrutiny for accuracy and reproducibility. However, there is a paucity of systematic and introductory surveys easily accessible to biologists when faced with a plethora of technical issues in digital image processing and analyses. The lack of clarity on this issue, compounded by debate over the methods abundant in the niche literature, frequently leads to further confusion for those whose primary expertise is not in digital image processing. Unfortunately, erroneous or misguided application of methods in biological imaging analyses is not uncommon, and this can lead to artificial inflation or suppression of biological significance – often unintentionally. The goal of this two-day hands-on workshop is to survey the fundamentals of how image pixel data can be used to extract biologically meaningful information. Participants will install necessary open source software on their own laptops (FAES can provide laptops if necessary) and will be given ample opportunity to work on actual images for truly hands-on learning experience.

 BioTech 63 - Protein-Protein Interactions

Proximity Ligation Assay (PLA) provides the ability to see and quantitate protein posttranslational modifications, define complex interaction, illuminate complex protein clusters or amplify low abundant single events. Duolink is a versatile tool for detection, quantification and localization of cytoplasmic signaling events. This 2 day course will introduce participants to the key concepts of Proximity Ligation Assay  and Duolink including technology development, assay design, antibody validation, best practices, trouble shooting and future applications. This workshop features hands-on lab exercises designed to provide participants with working knowledge of PLA & Duolink. Training slots are limited to 20, Registrations are First Come- First Serve basis.

Lecture Highlights

• Intro and History of PLA and Duolink

• Duolink Assay Workflow

• Assay design, Antibody selection and Validation

• Best Practices and Troubleshooting

• Novel Applications of PLA

• Future Directions, Multiplexing, IVD

• Data Analysis

Laboratory Highlights

• Cell Fixation and Permeabilization

• Antibody Incubation and Washing

• Ligation and Rolling Circle DNA Amplification

• Assay Imaging

• Results Analysis

 BioTech 64 - Imaging Flow Cytometry

This is a 3-day workshop on imaging flow cytometry focused on understanding how imaging flow cytometers work, experimental design and planning and hands on practice of running samples on the instrument on Day 1 and data analysis using image analysis software on day 2 and 3.  The workshop will also include 2 key note speakers showcasing data derived from imaging flow cytometers. 

WHO SHOULD ATTEND?
Specifically geared toward life scientists, this inetnsive hands-on workshop will survey basic and advanced topics in imaging flow cytometer sample preparation, data/image acquistion, processing and analysis.

This is an intensive hands-on workshop. FAES will provide laptops with necessary software for the duration of the course.

 BioTech 66 - Computational Drug Design and Discovery

Computational drug design and discovery has been a challenging task due to limitations in available computing resources. Public cloud computing facilities have dramatically changed this scenario, by bringing the most powerful computing systems within a click away, with unprecedented low cost options.

Objectives:
This hands-on training will introduce researchers to the concepts, methods and tools for structure and ligand based computational drug designing and discovery using the open source tools and the cloud computing facilities.

 BioTech 71 - Project Management Training for Scientist​
 BioTech 73 - Cloud Computing for Biomedical Researchers

Background:
Cloud offers computers with hundreds of cores and terabytes of memory, on a hourly basis, for a mere couple of dollars and on-demand, for anyone who can use a computer and internet. This democratizes the high performance computing that everybody can use.

Objectives:
Participants will create personal cloud computing accounts, instances (renting and using a windows machine and linux machine), set security, configure storage, create snapshots, create clusters, images, access instances and perform routine tasks.

 BioTech 74 - Advanced Transcriptomics (RNA-Seq) Analysis

Objectives:
Apart from performing the routine differential expression analysis using two different suite of tools, this hands-on training will help participants learn advanced RNA-Seq analysis techniques and tools for detecting snps, fusion genes, allele specific expressions, circular RNAs, viral/bacterial sequence identification, alternative polyadenylation and transcriptional regulatory network analysis.

Highlights:

  • Participants will use a Graphic User Interface based Linux Desktop environment, specially configured for advanced RNA-Seq analysis in the Amazon Cloud
  • Cloud image with fully configured advanced RNA-Seq tools, freely provided to participants
 BioTech 75 - Metagenomics Data Analysis

Objectives:
Metagenomics is gaining importance due to low cost next generation sequencing technologies. This training will introduce participants to the end-to-end solutions for analyzing metagenomic data, starting from data quality analysis, alignment, community profiling, taxonomic comparison and novel taxa discovery.

Highlights:
Participants will work with a Graphic User Interface based Linux Desktop environment in the Amazon Cloud, that is specially configured to run popular open source metagenomics analysis tools. Participants will be able to save and take home a copy of the fully configured Amazon Machine Image for their personal use after the training. Participants will also receive a cookbook style manual for all the hands-on exercises. After training support is also provided through exclusive members only forum.

BioTech 76 - Creating Plots, Graphs, and maps using R

 

Background:
R is the industry standard for creating scientific graphs and plots. There are several different R packages available for creating impressive plots, graphs and maps including plotly, ggplot2, ggvis, diagrammer - for diagrams, dygraphs - for time series data, leaflet - for plotting maps, graphviz - for graphs. This training will walk through participants in creating awesome, interactive, static, shareable plots using the popular R packages.

Objectives:
Participants will get a brief hands-on introduction to the R platform, followed by hands-on walkthrough for creating several different popular plots, graphs and maps like scatter plots, density plots, correlation plots, pca plots, surface plots, dot plots, star plots, circular plots, trees, heatmaps, panel graphs, 3D graphs, network graphs. We will start from formatting data and go all the way to loading data, setting parameters, creating the images and saving the outputs.

 BioTech 77 - Molecular Modeling and Molecular Dynamics

 

Background:
Predicting the effect of a mutation on the structure and function of a protein is not just for researchers with super-computer facilities. Thanks to public cloud computing options, anyone with basic molecular biology background can setup and run compute intensive computational modeling and dynamics experiments.

Objectives:

Participants will use popular open source tools and techniques necessary for conducting successful molecular modeling and dynamics experiments in the cloud.

BioTech 78 - Data Integration, Analysis and VisualizationObjectives

 

Data integration is a big problem in biomedical research, especially in the era of NGS data, BigData, “omics”, precision medicine etc. Network based approach is one of the interesting and efficient ways to integrate data. This hands-on training will introduce participants to network concepts, data preparation and integration methods, data analysis, exploration and visualization using Cytoscape and other open source tools. The training also includes a one day Bring-Your-Own-Data* clinic.

Hands-on Skills/Tools 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  

BioTech 80 - CAR T-Cells: Principles & Methods

Chimeric antigen receptor-modified T cells (CAR-T cells) are T cells engineered to target and eliminate a specific type of cancerous cells.  Substantial investments have been made in this field over the past few years due to the great promise this technology shows in targeting virtually any antigen-presenting tumor cell.  This course will combine lectures and hands-on training to introduce participants to the potential of CAR-T cells and the different approaches for the utilization of this technology in different applications along with techniques for the production and automation of manufacturing of CAR-T cells. This intensive training program also provides opportunity to particpants to network with experts in CAR-T field from both academia and industries. Each particpant will receive printed course materials.  

Lecture Topics

Introduction to the development and potential of CAR-T cell technology, different approaches for the manufacturing CAR-T cells, and potential obstacles in the implementation of this technology on a larger scale.

Laboratory Topics

CAR-T Cell manufacturing including the process of T cell isolation, activation, transduction, culturing, and reformulation.  We will also explore options for automation of the CAR-T cell manufacturing process.

BioTech 81 - Nanotechnology: Principles & Methods

In this three-day intensive training program, participants will learn the basics of nanotechnology in medicine and about the preparation and clinical use of different nanotechnologies. In laboratory sessions, participants will prepare and characterize two such systems.  These techniques will then be used in a bioassay to deliver material to cells in vitro.  This  training program also provides opportunity to particpants to network with experts in nanotechnology field from both academia and industries. Each particpant will receive printed course materials.

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