Computational Biology and BioinformaticsSharif Shuvo
Computational Biology and Bioinformatics is a rapidly developing multi-disciplinary field. The systematic achievement of data made possible by genomics and proteomics technologies has created a tremendous gap between available data and their biological interpretation.
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
Computational Biology and BioinformaticsSharif Shuvo
Computational Biology and Bioinformatics is a rapidly developing multi-disciplinary field. The systematic achievement of data made possible by genomics and proteomics technologies has created a tremendous gap between available data and their biological interpretation.
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
this presentation is about bioinformatics. the contents of bioinformatics are as under:
1.Introduction to bioinformatics.
2.Why bioinformatics is necessary?
3.Goals of bioinformatics
4.Field of bioinformatics
5.Where bioinformatics help?
6.Applications of bioinformatics
7.Software and tools of bioinformatics
8.References
An introduction to bioinformatics practices and aims will be given and contrasted against approaches from other fields. Most importantly, it will be discussed how bioinformatics fits into the discovery cycle for hypothesis driven neuroscience research.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
Introduction to Synthetic Genome
SYNTHETIC GENOMICS Study of Invitro chemical synthesis of genetic material i.e., DNA in the form of oligonucleotides, genes, or genomes with Computational techniques for its design. SYNTHETIC GENOME Artificially synthesised genome (invitro)
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVE OF BIOINFORMATIC
TOOLS OF BIOINFORMATICS
PROCEDURE AND TOOLS OF BIOINFORMATIC
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
Tutorial 1: Your First Science App - Araport Developer WorkshopVivek Krishnakumar
Slide deck pertaining to Tutorial 1 of the Araport Developer Workshop conducted at TACC, Austin TX on November 5, 2014.
Presented by Vivek Krishnakumar
this presentation is about bioinformatics. the contents of bioinformatics are as under:
1.Introduction to bioinformatics.
2.Why bioinformatics is necessary?
3.Goals of bioinformatics
4.Field of bioinformatics
5.Where bioinformatics help?
6.Applications of bioinformatics
7.Software and tools of bioinformatics
8.References
An introduction to bioinformatics practices and aims will be given and contrasted against approaches from other fields. Most importantly, it will be discussed how bioinformatics fits into the discovery cycle for hypothesis driven neuroscience research.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
Introduction to Synthetic Genome
SYNTHETIC GENOMICS Study of Invitro chemical synthesis of genetic material i.e., DNA in the form of oligonucleotides, genes, or genomes with Computational techniques for its design. SYNTHETIC GENOME Artificially synthesised genome (invitro)
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVE OF BIOINFORMATIC
TOOLS OF BIOINFORMATICS
PROCEDURE AND TOOLS OF BIOINFORMATIC
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
Tutorial 1: Your First Science App - Araport Developer WorkshopVivek Krishnakumar
Slide deck pertaining to Tutorial 1 of the Araport Developer Workshop conducted at TACC, Austin TX on November 5, 2014.
Presented by Vivek Krishnakumar
Computational Approaches to Systems BiologyMike Hucka
Presentation given at the Sydney Computational Biologists meetup on 21 August 2013 (http://australianbioinformatics.net/past-events/2013/8/21/computational-approaches-to-systems-biology.html).
Analytics meets Big Data – R/Python auf der Hadoop/Spark-PlattformRising Media Ltd.
Big Data verändert nicht nur die Unternehmens-IT fundamental, sondern auch die Arbeit des Analysten. Die klassischen Analysten sehen sich im Zuge des Wandels zu einer datengetriebenen Unternehmenskultur mit neuen Anforderungen und ungewohnten technologischen Plattformen konfrontiert. Sie müssen als Data Scientist fachliche Fragestellungen unter dem Aspekt der Big Data-Technologien umsetzen, visualisieren und aus den Daten Werte generieren. Anhand eines konkreten Use Cases, der Programmierung eines Recommender-Systems, zeigen wir Ansätze, wie sich die gewohnten Vorgehensweisen und Werkzeuge eines Analysten (namentlich R und Python) mit einer Big Data-Technologie (Spark) kombinieren lassen. Ziel ist es, dem Analysten den Einstieg in die Big Data-Welt zu erleichtern. Wir demonstrieren die Arbeit mit diesem Toolset an anschaulichen Beispielen in einem interaktiven Workshop-Format und laden zur Diskussion und Nachahmung dieser Vorgehensweise ein. Der Workshop richtet sich an Teilnehmer mit Grundkenntnissen aus den Bereichen analytische Methoden und Machine Learning sowie R oder Python. Der Workshop wird auf der Spark-Plattform durchgeführt. Zu Spark werden keine Kenntnisse vorausgesetzt.
Apps for Science - Elsevier Developer Network Workshop 201102remko caprio
This presentation is an introduction into programming OpenSocial Gadgets for Science.
1. overview of apps
2. social networks
3. opensocial
4. SciVerse Platform
5. SciVerse APIs
6. Coding OpenSocial Gadgets for SciVerse
7. Resources
Do you know what k-Means? Cluster-Analysen Harald Erb
Cluster-Analysen sind heute "Brot und Butter"-Analysetechniken mit Verfahren, die zur Entdeckung von Ähnlichkeitsstrukturen in (großen) Datenbeständen genutzt werden, mit dem Ziel neue Gruppen in den Daten zu identifizieren. Der K-Means-Algorithmus ist dabei einer der einfachsten und bekanntesten unüberwachten Lernverfahren, das in verschiedenen Machine Learning Aufgabenstellung einsetzbar ist. Zum Beispiel können abnormale Datenpunkte innerhalb eines großen Data Sets gefunden, Textdokumente oder Kunden¬segmente geclustert werden. Bei Datenanalysen kann die Anwendung von Cluster-Verfahren ein guter Einstieg sein bevor andere Klassifikations- oder Regressionsmethoden zum Einsatz kommen.
In diesem Talk wird der K-Means Algorithmus samt Erweiterungen und Varianten nicht im Detail betrachtet und ist stattdessen eher als ein Platzhalter für andere Advanced Analytics-Verfahren zu verstehen, die heute „intelligente“ Bestandteile in modernen Softwarelösungen sind bzw. damit kombiniert werden können. Anhand von zwei Kurzbeispielen wird live gezeigt: (1) Identifizierung von Kunden-Cluster mit einem Big Data Discovery Tool und Python (Jupyter Notebook) und (2) die Realisierung einer Anomalieerkennung direkt im Echtzeitdatenstrom mit einer Stream Analytics Lösung von Oracle.
In this presentation its given an introduction about Data Science, Data Scientist role and features, and how Python ecosystem provides great tools for Data Science process (Obtain, Scrub, Explore, Model, Interpret).
For that, an attached IPython Notebook ( http://bit.ly/python4datascience_nb ) exemplifies the full process of a corporate network analysis, using Pandas, Matplotlib, Scikit-learn, Numpy and Scipy.
Mathai Joseph, Advisor, Tata Consultancy Service discusses about Alan Turing at the Grand Launch of Alan Turing Centenary Celebrations at Persistent Systems
Im Kontext von IoT spielt die Gewinnung und Verarbeitung von großen Datenmengen, z.B. von Sensoren eine große Rolle. Die Rohdaten alleine machen aber noch lange keine smarten Systeme. Aus Daten werden Informationen aus Informationen wird Wissen und aus Wissen resultieren Entscheidungen - im besten Fall. Neben der technischen Herausforderungen im Umgang mit BigData rückt die „schlaue Auswertung" derselben (Digitale Analyse) immer mehr in den Vordergrund und zeigt die Grenzen des Könnens vieler Unternehmen auf. Kein Wunder also, dass dem Berufsbild des Data Scientisten eine wachsende Bedeutung zukommt. Nicht umsonst benannte das Harvard Business Review diesen als „The sexiest job of the 21st Century“.
Die Digital Analytics Assocations e.V. (DAA) treibt gezielt Fach- und Führungskräfte sowie Unternehmen die Professionalisierung von Digitalen Analysten und Data Scientists voran.
Frank Pörschmann, Mitglied des Vorstands des DAA e.V., erzählt in diesem Vortrag etwas über
- den Unterschied zwischen BigData, SmartData und Data Analytics
- Datenökonomie
- das Berufsbild des Data Scientist / Digitalen Analysten
- Aus- und Fortbildungsmöglichkeiten
Journal of Computational Systems Biology (JCSB) is an open access online journal which aims to publish peer reviewed research articles and short communications in all aspects of computational biology and bioinformatics. JCSB comprehend the broad spectrum of computational bioscience including biological databases and bioalgorithms.
Lawrence berkeley national laboratory sep 2015 - Jupyter Talk
Scientific facilities are increasingly generating large data sets. Next-generation scientific productivity relies on user-friendly tools and efficient, effective and seamless access to resources and data. Traditional approaches to research and software development for science focus on the hardware and software of the machine and do not consider the user. In this talk, I will highlight a different approach to building software for scientific users by including user knowledge in the process. I will illustrate a few example projects where this has been used to date.
GIthub repository: https://github.com/Carreau/talks/tree/master/labtech-2015
Centre for Genomic Regulation Talk February 2024.pptxNick Brown
Presentation I recently gave at the Centre for Genomic Regulation in Barcelona - providing a glimpse into my career in AstraZeneca over 20 years with some advice for younger data scientists getting into the field.
Updated Agenda- CRISPR Congress in Berlin, 24-26 October 2016Diane McKenna
The Only Industry Event Solely Dedicated to Optimising the Applications CRISPR Precision Genome Editing in Europe.
Overcome key specificity, efficiency & delivery challenges to pioneer drug discovery, biomedical research and therapeutic applications of precision genome engineering. With customisation of CRISPR design paramount, join leading biopharma and academic figureheads as they reveal advanced methodology, strategies and clinical timelines to fulfil the revolutionary promise of precision genome editing.
Molecular scaffolds are special and useful guides to discovery, poster (36x54"). Presented at ACS National Meeting SciMix in Indianapolis, Sep 9, 2013.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
8. Darwin’s theory of evolution, the genetic bases of humans(homo sapiens) found
from apes..
9. 1953- structure of DNA
discovered
1995- first bacterial
genome
2001- first human
genome drafting starts
2004- human genome
completed
2004- computer
platform used
2010- bench-top next
gen sequencers used
13. Use of computer stimulations of biological systems,
including cellular subsystems (network metabolites,
enzymes, metabolism, signal transduction pathways, gene
regulatory networks) to analyze and visualize complex
connections of these cellular processes...
Tasks- cellular model
- multi-cellular organism stimulation
- protein folding
- brain model
- immune systems
- virtual liver
- modeling of infectious disease
14. Computer assisted surgical planning
on 3-D liver
HEPATOSYS- programme supporting
projects looking at cellular networks of the
liver cell.
17. To the era of disease free kids....
No human and animal testing of drugs
Cancer-free society
Looking inside humans- human genomics
drafts....
For us- computer dentists!!!
t involves the use of computer simulations of biological systems, including cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks), to both analyze and visualize the complex connections of these cellular processes.
design and creation of dental restorations including crowns, crown lays, veneers, inlays and onlays, fixedbridges, dental implant restorations, dentures (removable or fixed), and orthodontic appliances