The document is a script for a randomized exam webpage that will display 4 images randomly selected from a pool of 713 images.
The script uses JavaScript to generate a random number between 1-713 to select the image source for each image displayed. It also includes some random text between elements.
The purpose is to randomly display a set of images on an exam webpage to prevent students from sharing answers.
Next Generation Sequencing Informatics - Challenges and OpportunitiesChung-Tsai Su
Genetic data is the foundation of precision medicine. Next Generation Sequencing(NGS) enable us to get our whole genome data in affordable cost. How to process huge amount of NGS data effectively ?
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
"Microbial Genomics @NIST" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Nathan Olson from NIST.
Examining gene expression and methylation with next gen sequencingStephen Turner
Slides on RNA-seq and methylation studies using next-gen sequencing given at the University of Miami Hussman Institute for Human Genomics "Genetic Analysis of Complex Human Diseases" course in 2012 (http://hihg.med.miami.edu/educational-programs/analysis-of-complex-human-diseases/genetic-analysis-of-complex-human-diseases/)
Presentation carried out by CNAG's director, Ivo Gut, at the course: Identification and analysis of sequence variants in sequencing projects: fundamentals and tools.
Presentation by Scott Woodman, MD, PhD. Presented at the 2018 Eyes on a Cure: Patient & Caregiver Symposium, hosted by the Melanoma Research Foundation's CURE OM initiative.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Course: Bioinformatics for Biologiacl Researchers (2014).
Session: 3.1- Introduction to Metagenomics. Applications, Approaches and Tools.
Statistics and Bioinformatisc Unit (UEB) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Next Generation Sequencing Informatics - Challenges and OpportunitiesChung-Tsai Su
Genetic data is the foundation of precision medicine. Next Generation Sequencing(NGS) enable us to get our whole genome data in affordable cost. How to process huge amount of NGS data effectively ?
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
"Microbial Genomics @NIST" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Nathan Olson from NIST.
Examining gene expression and methylation with next gen sequencingStephen Turner
Slides on RNA-seq and methylation studies using next-gen sequencing given at the University of Miami Hussman Institute for Human Genomics "Genetic Analysis of Complex Human Diseases" course in 2012 (http://hihg.med.miami.edu/educational-programs/analysis-of-complex-human-diseases/genetic-analysis-of-complex-human-diseases/)
Presentation carried out by CNAG's director, Ivo Gut, at the course: Identification and analysis of sequence variants in sequencing projects: fundamentals and tools.
Presentation by Scott Woodman, MD, PhD. Presented at the 2018 Eyes on a Cure: Patient & Caregiver Symposium, hosted by the Melanoma Research Foundation's CURE OM initiative.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Course: Bioinformatics for Biologiacl Researchers (2014).
Session: 3.1- Introduction to Metagenomics. Applications, Approaches and Tools.
Statistics and Bioinformatisc Unit (UEB) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
An Introduction to Bioinformatics
Drexel University INFO648-900-200915
A Presentation of Health Informatics Group 5
Cecilia Vernes
Joel Abueg
Kadodjomon Yeo
Sharon McDowell Hall
Terrence Hughes
Inside Out and Upside Down - FOO Camp 2016 - Peter CoffeePeter Coffee
Four "truths" of IT are still true enough to yield ROI by pursuing their further development -- but you'll never realize how much you left on the table by failing to appreciate their transformation in a massively connected world.
Discovery on Target 2014 - The Industry's Preeminent Event on Novel Drug TargetsJaime Hodges
Cambridge Healthtech Institute's 12th Annual Discovery on Target will showcase current and emerging “hot” targets for the pharmaceutical industry, October 8 – 10, 2014 in Boston, MA. Spanning three days, the meeting will bring together more than 900 global attendees, including scientists/technologists, executives, directors, and managers from biopharma, academic, and healthcare organizations. In 2014 the event is comprised of 14 conference tracks which include Epigenetic Readers, Ubiquitin Proteasome, Big Data Discovery, GPCR Drug Discovery, RNAi-Screens-Functional-Genomics, PPI Targets, Protein-Targets, Histone-Methyltransferases-Demethylases, Drug Transporters, Maximizing Efficiency, GPCR Therapeutics, Genomics Screening, Cancer Metabolism and Membrane Production. The 2014 event will offer 200+ scientific presentations across 14 conference tracks, 1 Symposium and 15 conference short courses, 40+ interactive breakout discussion groups, an exhibit hall of 40+ companies, and dedicated poster viewing and networking sessions.
*Watch the video at the end of the presentation
Seminar led by Dr. Xavier de la Cruz, ICREA Research Professor. Head of the Translational Bioinformatics in Neuroscience group of VHIR, at VHIR (22nd November 2012).
Content: The need to identify the pathological character of mutations may arise in different contexts in biomedical research. However, the methods available to address this problem essentially depend on the number of cases under analysis. When we work with only a few mutations we can use an artisan-like approach, where all information available on protein sequence, structure and function is manually retrieved and studied. However, when we need to characterize many variants, as can be the case in exome projects, faster methods are required to assess their pathogenicity. In my talk I will illustrate the principles underlying these two approaches with examples from the study of Fabry disease mutations, resulting from our collaborative work at the VHIR.
dkNET Webinar: Multi-Omics Data Integration for Phenotype Prediction of Type-...dkNET
Abstract
Omics techniques (e.g., i.e., transcriptomics, genomics, and epigenomics) report quantitative measures of more than tens of thousands of biological features and provide a more comprehensive molecular perspective of studied diabetes mechanisms compared to transitional approaches. Identifying representative molecular signatures from the tremendous number of biological features becomes a central problem in utilizing the data for clinical decision-making. Exploring the complex causal relations of the identified representative molecular signatures and diabetes phenotypes can be the most effective and efficient ways to improve the understanding of diabetes and assess the cause of diabetes for the new patients with already collected data influencing (e.g., TEDDY project). However, due to the unavoidable patient heterogeneity, statistical randomness, and experimental noise in the high-dimension, low-sample-size omics data of the diabetic patients, utilizing the available data for clinical decision-making remains an ongoing challenge for many researchers. To overcome the limitations, in this study we developed (1) a generative adversarial network (GAN)-based model to generate synthetic omics data for the samples with few omics profiles available; (2) a deep learning-based fusion network model for phenotype prediction of type-1 diabetes; (3) a long short-term memory (LSTM)-based model for predicting outcomes of islet autoantibody and persistent positivity. The models are tested on the multi-omics data in TEDDY project.
Presenter: Wei Zhang, Ph.D. Assistant Professor, Department of Computer Science & Genomics and Bioinformatics Cluster, University of Central Florida
Upcoming webinars schedule: https://dknet.org/about/webinar
This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of implementing genomics in the clinic. It uniquely illustrates the mutual influence of those areas and the need to therefore consider the needs, challenges and opportunities of both - from next-generation sequencing and variant interpretation to insurance reimbursement and electronic health records - throughout the entire research process.Learn more at http://www.clinicalgenomeconference.com
Meaningful (meta)data at scale: removing barriers to precision medicine researchNolan Nichols
Randomized controlled trials (RCTs) are the gold standard for evaluating therapeutics in patient populations. The data collected during RCTs include a wealth of clinical measures, biomarkers, and tissue samples – the analysis of which can lead to the approval of new medicines that improve the lives of patients. The secondary use of these data can also fuel the discovery of novel targets and biomarkers that support precision medicine, but a lack of metadata standards creates substantial barriers to reuse.
For this talk, I will discuss the challenges that arise when aggregating diverse types of data from a large number of RCTs and present a case study in how to apply (meta)data standards for the scalable curation and integration of these data into an analysis ready form.
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
Normal Labour/ Stages of Labour/ Mechanism of LabourWasim Ak
Normal labor is also termed spontaneous labor, defined as the natural physiological process through which the fetus, placenta, and membranes are expelled from the uterus through the birth canal at term (37 to 42 weeks
Embracing GenAI - A Strategic ImperativePeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
8. Lab for Bioinformatics and computational genomics
107 106 105 104 103 102 101 1108109
Full genome bp
G
E
N
E
T
I
C
Whole-genome
sequencing
Enrichment seq
(Exome)
PCR
Enrichment
Targeted Panels
Instrument and Assay providers
CLIA Lab service providers
9.
10.
11.
12.
13.
14. Personalized Medicine
• The use of diagnostic tests (aka biomarkers) to identify in advance
which patients are likely to respond well to a therapy
• The benefits of this approach are to
– avoid adverse drug reactions
– improve efficacy
– adjust the dose to suit the patient
– differentiate a product in a competitive market
– meet future legal or regulatory requirements
• Potential uses of biomarkers
– Risk assessment
– Initial/early detection
– Prognosis
– Prediction/therapy selection
– Response assessment
– Monitoring for recurrence
15. Biomarker
First used in 1971 … An objective and
« predictive » measure … at the molecular
level … of normal and pathogenic processes
and responses to therapeutic interventions
Characteristic that is objectively measured and
evaluated as an indicator of normal biologic
or pathogenic processes or pharmacologic
response to a drug
A biomarker is valid if:
– It can be measured in a test system with well
established performance characteristics
– Evidence for its clinical significance has been
established
16. Rationale 1:
Why now ? Regulatory path becoming more clear
There is more at stake than
efficient drug
development. FDA
« critical path initiative »
Pharmacogenomics
guideline
Biomarkers are the
foundation of « evidence
based medicine » - who
should be treated, how
and with what.
Without Biomarkers
advances in targeted
therapy will be limited and
treatment remain largely
emperical. It is imperative
that Biomarker
development be
accelarated along with
therapeutics
17. Why now ?
First and maturing second generation molecular
profiling methodologies allow to stratify clinical
trial participants to include those most likely to
benefit from the drug candidate—and exclude
those who likely will not—pharmacogenomics-
based
Clinical trials should attain more specific results
with smaller numbers of patients. Smaller
numbers mean fewer costs (factor 2-10)
An additional benefit for trial participants and
internal review boards (IRBs) is that
stratification, given the correct biomarker, may
reduce or eliminate adverse events.
18. Molecular Profiling
The study of specific patterns (fingerprints) of proteins,
DNA, and/or mRNA and how these patterns correlate
with an individual's physical characteristics or
symptoms of disease.
19. Generic Health advice
• Exercise (Hypertrophic Cardiomyopathy)
• Drink your milk (MCM6 Lactose intolarance)
• Eat your green beans (glucose-6-phosphate
dehydrogenase Deficiency)
• & your grains (HLA-DQ2 – Celiac disease)
• & your iron (HFE - Hemochromatosis)
• Get more rest (HLA-DR2 - Narcolepsy)
20. Generic Health advice (UNLESS)
• Exercise (Hypertrophic Cardiomyopathy)
• Drink your milk (MCM6 Lactose intolarance)
• Eat your green beans (glucose-6-phosphate
dehydrogenase Deficiency)
• & your grains (HLA-DQ2 – Celiac disease)
• & your iron (HFE - Hemochromatosis)
• Get more rest (HLA-DR2 - Narcolepsy)
21. Generic Health advice (UNLESS)
• Exercise (Hypertrophic Cardiomyopathy)
• Drink your milk (MCM6 Lactose intolerance)
• Eat your green beans (glucose-6-phosphate
dehydrogenase Deficiency)
• & your grains (HLA-DQ2 – Celiac disease)
• & your iron (HFE - Hemochromatosis)
• Get more rest (HLA-DR2 - Narcolepsy)
22. Generic Health advice (UNLESS)
• Exercise (Hypertrophic Cardiomyopathy)
• Drink your milk (MCM6 Lactose intolerance)
• Eat your green beans (glucose-6-phosphate
dehydrogenase Deficiency)
• & your grains (HLA-DQ2 – Celiac disease)
• & your iron (HFE - Hemochromatosis)
• Get more rest (HLA-DR2 - Narcolepsy)
32. First Generation Molecular Profiling
• Flow cytometry correlates surface markers,
cell size and other parameters
• Circulating tumor cell assays (CTC’s)
quantitate the number of tumor cells in the
peripheral blood.
• Exosomes are 30-90 nm vesicles secreted by
a wide range of mammalian cell types.
• Immunohistochemistry (IHC) measures
protein expression, usually on the cell
surface.
33.
34.
35.
36. First Generation Molecular Profiling
• Gene sequencing for mutation detection
• Microarray for m-RNA message detection
• RT-PCR for gene expression
• FISH analysis for gene copy number
• Comparative Genome Hybridization (CGH) for
gene copy number
37. Basics of the “old” technology
• Clone the DNA.
• Generate a ladder of labeled (colored)
molecules that are different by 1 nucleotide.
• Separate mixture on some matrix.
• Detect fluorochrome by laser.
• Interpret peaks as string of DNA.
• Strings are 500 to 1,000 letters long
• 1 machine generates 57,000 nucleotides/run
• Assemble all strings into a genome.
51. Lab for Bioinformatics and computational genomics
The Technical Feasibility Argument
The Quality Argument
The Price Argument
The Logistics Argument
54. Lab for Bioinformatics and computational genomics
Recreational genomics
• Experimental designs are outdated by technological advances
• Genetic background (reference genome) as a concept will need to be
updated
• Traits dependent on multiple loci are “complicated”: educate and
provide tools to deal with it
56. Lab for Bioinformatics and computational genomics
Recreational genomics
• Eye color … why not the ear wax/asparagus or unibrown example
• … metabolize nutrients (newborns ?)
• … metabolize drugs in case you need it urgently ?
58. Lab for Bioinformatics and computational genomics
Recreational genomics
“several 23andMe users have reported taking the FDA’s
advice of reviewing their genetic results with their
physicians, only to find the doctors unprepared, unwilling,
or downright hostile to helping interpret the data”
69. Lab for Bioinformatics and computational genomics
Everyone should have the power and legitimacy to
be able to discover, develop and find new things
about their own genome data.
Intelligent exploration, experimentation and trial to
push the boundaries of knowledge are a basic
human right.
PGMv2: Personal Genomics Manifesto
70. Lab for Bioinformatics and computational genomics
Personal genome data access should be
affordable to all irrespective of nationality, gender,
social background or any other circumstance.
Not having access to a personal genetic test is in
itself a new kind of discrimination.
PGMv2: Personal Genomics Manifesto
71. Lab for Bioinformatics and computational genomics
Whether one wants to share genome data or keep it
private should be a matter of personal choice.
Whatever attitude a person has towards personal
genome privacy, it should be utterly respected.
Corporate interest can never compromise any human
right. Laws must fully protect individual human rights of
equality for every person, irrespective of predicted risks
from genetic data.
PGMv2: Personal Genomics Manifesto
72. Lab for Bioinformatics and computational genomics
Stating that genetic tests merely provide non-
clinical information misses the point of what
personal genomics is all about.
Most genomic information is uninterpretable and
may well be meaningless. But those are not
reasons to deny it to people.
Genetic test results are not unrelated to
someone’s health, one’s ability to respond to
certain drugs and one’s ethnic ancestry.
PGMv2: Personal Genomics Manifesto
73. Lab for Bioinformatics and computational genomics
Education in risks and opportunities for personal
genetic testing should be the primary aim of
policy makers.
Restricting access to interested people makes
no sense and it is virtually impossible to ensure.
Access to personal genomics data and tools for
its interpretation should become accessible to
everyone.
PGMv2: Personal Genomics Manifesto
82. First Generation Molecular Profiling
• Gene sequencing for mutation detection
• Microarray for m-RNA message detection
• RT-PCR for gene expression
• FISH analysis for gene copy number
• Comparative Genome Hybridization (CGH) for
gene copy number
84. First Generation Molecular Profiling
• Gene sequencing for mutation detection
• Microarray for m-RNA message detection
• RT-PCR for gene expression
• FISH analysis for gene copy number
• Comparative Genome Hybridization (CGH) for
gene copy number
85.
86. Translational Medicine: An inconvenient truth
• 1% of genome codes for proteins, however
more than 90% is transcribed
• Less than 10% of protein experimentally
measured can be “explained” from the
genome
• 1 genome ? Structural variation
• > 200 Epigenomes ??
• Space/time continuum …
87. Translational Medicine: An inconvenient truth
• 1% of genome codes for proteins, however
more than 90% is transcribed
• Less than 10% of protein experimentally
measured can be “explained” from the
genome
• 1 genome ? Structural variation
• > 200 Epigenomes …
• “space/time” continuum