Walks through a couple of KNIME Workflows for working with HTS Data.
The workflows are derived from the work described in this publication: https://f1000research.com/articles/6-1136/v2
Case Studies in advanced analytics with RWit Jakuczun
A talk I gave at SQLDay 2017:
About 1,5 years ago Microsoft finalised acquisition of Revolution Analytics – a provider of software and services for R. In my opinion this was one of the most important event for R community. Now it is crucial to present its capabilities to SQL Server community. It will be beneficial for both parties. I will present three case studies: cash optimisation in Deutsche Bank, midterm model for energy prices forecasting, workforce demand optimising. The case studies were implemented with our analytical workflow R Suite that will be also shortly presented.
Speaker: Pierre Richemond, Data Science Institute of Imperial College
Title: Cutting edge generative models: Applications and implications
Abstract: This talk will examine recent developments in deep learning content generation at scale. Whether it be images or text, the latest methods have now reached a level of quality making it hard to discriminate between human- and AI-generated content. We will review recent examples of such generative models, and put their significance in a broader context, in light of such powerful tools’ potential for dual use.
Bio: Pierre is currently researching his PhD in deep reinforcement learning at the Data Science Institute of Imperial College. He also teaches Deep Learning at the Graduate School, and helps to run the Deep Learning Network and organises thematic reading groups. His background is in mathematics - he has studied electrical engineering at ENST, probability theory and stochastic processes at Universite Paris VI - Ecole Polytechnique, and business management at HEC.
Case Studies in advanced analytics with RWit Jakuczun
A talk I gave at SQLDay 2017:
About 1,5 years ago Microsoft finalised acquisition of Revolution Analytics – a provider of software and services for R. In my opinion this was one of the most important event for R community. Now it is crucial to present its capabilities to SQL Server community. It will be beneficial for both parties. I will present three case studies: cash optimisation in Deutsche Bank, midterm model for energy prices forecasting, workforce demand optimising. The case studies were implemented with our analytical workflow R Suite that will be also shortly presented.
Speaker: Pierre Richemond, Data Science Institute of Imperial College
Title: Cutting edge generative models: Applications and implications
Abstract: This talk will examine recent developments in deep learning content generation at scale. Whether it be images or text, the latest methods have now reached a level of quality making it hard to discriminate between human- and AI-generated content. We will review recent examples of such generative models, and put their significance in a broader context, in light of such powerful tools’ potential for dual use.
Bio: Pierre is currently researching his PhD in deep reinforcement learning at the Data Science Institute of Imperial College. He also teaches Deep Learning at the Graduate School, and helps to run the Deep Learning Network and organises thematic reading groups. His background is in mathematics - he has studied electrical engineering at ENST, probability theory and stochastic processes at Universite Paris VI - Ecole Polytechnique, and business management at HEC.
Managing large (and small) R based solutions with R SuiteWit Jakuczun
The presentation I gave at DataMass Gdańsk Summit in 2017:
R is a great tool for data scientist. Being very dynamic and popular is now one of the most important technology on the market. Unfortunately out-of-the-box R is not suited for large scale applications. I will present R Suite that is an open-source solution developed by us for us to manage R development process.
Overview of the US National Science Foundation Cloud and Autonomic Computing Industry/University Cooperative Research Center testbed activities on the US NSF Chameleon, Cloudlab and XSEDE resources.
The NSF CAC will use its industry/university connections to promote and foster open cloud standards & interoperability testbeds using internal and external resources.
Specific projects have been proposed and approved on two new NSF computer-science-oriented cloud “testbed as a service” resources, Chameleon and CloudLab, which have recently been funded to replace the FutureGrid project.
These testbeds will be open to all researchers who wish to cooperate with us on cloud interoperability, performance, standards or general cloud functionality testing within the context of the approved projects.
Both US domestic and international participants are welcome, as long as you’re willing to work on interoperability topics and share your results.
Opportunties for involvement in the CAC by commercial companies also exist, as described at http://nsfcac.org
Know your R usage workflow to handle reproducibility challengesWit Jakuczun
R is used in a vast ways. From pure ad-hoc by hobbysts to an organized and structured way in an enterprise. Each way of R usage brings different reproducibility challenges. Going through range of typical workflows we will show that understanding reproducibility must start with understanding your workflow. Presenting workflows we will show how we deal reproducibiilty challenges with open-source R Suite (http://rsuite.io) solution developed by us to support our large scale R development.
Quick and Dirty: Scaling Out Predictive Models Using Revolution Analytics on ...Revolution Analytics
[Presentation by Skylar Lyon at DataWeek 2014, September 17 2014.]
I recently faced the task of how to scale out an existing analytics process. The schedule was compressed - it always is in my world. The data was big - 400+ million rows waiting in database. What did I do? I offered my favorite type of solution - quick and dirty.
At the outset, I wasn't sure how easy it would be. Nor was I certain of realized performance gains. But the concept seemed sound and the exercise fun. Let's move the compute to the data via Revolution R Enterprise for Teradata.
This presentation outlines my approach in leveraging a colleague's R models as I experimented with running R in-database. Would my path lead to significant improvement? Could it be used to productionalize the workflow?
Massively Scalable Computational Finance with SciDBParadigm4Inc
Hedge funds, investment managers and prop shops need to keep pace with rapidly growing data volumes from many sources.
SciDB—an advanced computational database programmable from R and Python—scales out to petabyte volumes and facilitates rapid integration of diverse data sources. Open source and running on commodity hardware, SciDB is extensible and scales cost effectively.
Attend this webinar to learn how quants and system developers harness SciDB’s massively scalable complex analytics to solve hard problems faster. SciDB’s native array storage is optimized for time-series data, delivering fast windowed aggregates and complex analytics, without time-consuming data extraction.
Webinar presenters will demonstrate real world use cases, including the ability to quickly:
1. Generate aggregated order books across multiple exchanges
2. Create adjusted continuous futures contracts
3. Analyze complex financial networks to detect anomalous behavior
Graph Databases and Machine Learning | November 2018TigerGraph
Graph Database and Machine Learning: Finding a Happy Marriage. Graph Databases and Machine Learning
both represent powerful tools for getting more value from data, learn how they can form a harmonious marriage to up-level machine learning.
Raster Algebra mit Oracle Spatial und uDigKarin Patenge
Im Foliensatz ist die Integration von Oracle Spatial mit Open Source Technolgien beschrieben. Am Beispiel von uDig wird Schritt-für-Schritt aufgezeigt, wie es zusammen mit Oracle Spatial für die Rasterdatenanalyse eingesetzt werden hier. Beispielhaft wird ein Vegetationsindex (NVDI) berechnet.
Bei Interesse gern auch weiterlesen auf dem Oracle Spatial Blog (http://oracle-spatial.blogspot.com).
Bob Jones, CERN & HNSciCloud Coordinator gives an update on the HNSciCloud Pre-Commercial Procurement which is now in its Solution Prototyping phase. The presentation includes also an overview of the prototypes under development.
Full Webinar: https://info.tigergraph.com/graph-gurus-21
In this Graph Gurus episode, we:
Explain the architecture and technical implementation for a TigerGraph + Spark graph-enhanced Machine Learning pipeline
Use TigerGraph both before training to extract (graph and non-graph) features and after training to apply the model on streaming data
Use Spark to train and tune machine learning models at scale
Present a solution in production at China Mobile that detects and prevents phone-based scams using machine learning with TigerGraph
Demo the data flow between Spark and TigerGraph via TigerGraph’s JDBC driver
Sr. Architect Pradeep Reddy, from Qubole, presents the state of Data Science in the enterprise industries today, followed by deep dive of an end-to-end real world machine learning use case. We'll explore the best practices and challenges of big data operations when developing new machine learning features and advanced analytics products at scale in the cloud.
This presentation, given by Bob Jones, CERN & HNSciCloud Coordinator, at the ESA-ESPI Workshop on “Space Data & Cloud Computing Infrastructures: Policies and Regulations”, describes what are the challenges and needs of the cloud users and explains how an hybrid cloud model can support them.
Developing Your Own Flux Packages by David McKay | Head of Developer Relation...InfluxData
Flux is easy to contribute to, and it is easy to share functions and libraries of Flux code with other developers. Although there are many functions in the language, the true power of Flux is its ability to be extended with custom functions. In this session, David will show you how to write your own custom function to perform some new analytics.
SAMOA: A Platform for Mining Big Data Streams (Apache BigData North America 2...Nicolas Kourtellis
A general overview of the APACHE SAMOA platform for mining big data streams using machine learning algorithms running on distributed stream processing platforms such as Apache STORM, Apache Flink, Apache Samza and Apache Apex.
Results are shown from experimentation with VHT, the Vertical Hoeffding Tree proposed in "VHT: Vertical Hoeffding Tree." N. Kourtellis, G. De Francisci Morales, A. Bifet, A. Mordupo. IEEE BigData 2016.
Presentation in APACHE BIG DATA North America 2016
Гостевая лекция Института биоинформатики. Подробнее: http://bioinformaticsinstitute.ru/lectures/1218
Несмотря на несерьезное название, на лекции разговор пойдет о важной проблеме в работе биоинформатика, почти любая реальная задача которого связана с обработкой и анализом больших данных. И решить задачу нужно не только правильно, но и эффективно. Процесс решения можно условно разделить на две части: «придумать», как решать, и «обучить» этому компьютер. И на лекции речь пойдет именно об эффективном «обучении».
Наивно реализованные алгоритмы работают неприемлемо долго, когда дело доходит до гигабайтов реальных данных. От биоинформатика уже требуются не просто базовые навыки программирования, но и знание технических нюансов. И даже у профессионального программиста уйдет немало времени, например, чтобы выгодно использовать возможности Hadoop при работе с Big Data. Так можно ли современному ученому обойтись без тщательного изучения кучи языков, библиотек и фреймворков и сосредоточиться именно на решении?
Managing large (and small) R based solutions with R SuiteWit Jakuczun
The presentation I gave at DataMass Gdańsk Summit in 2017:
R is a great tool for data scientist. Being very dynamic and popular is now one of the most important technology on the market. Unfortunately out-of-the-box R is not suited for large scale applications. I will present R Suite that is an open-source solution developed by us for us to manage R development process.
Overview of the US National Science Foundation Cloud and Autonomic Computing Industry/University Cooperative Research Center testbed activities on the US NSF Chameleon, Cloudlab and XSEDE resources.
The NSF CAC will use its industry/university connections to promote and foster open cloud standards & interoperability testbeds using internal and external resources.
Specific projects have been proposed and approved on two new NSF computer-science-oriented cloud “testbed as a service” resources, Chameleon and CloudLab, which have recently been funded to replace the FutureGrid project.
These testbeds will be open to all researchers who wish to cooperate with us on cloud interoperability, performance, standards or general cloud functionality testing within the context of the approved projects.
Both US domestic and international participants are welcome, as long as you’re willing to work on interoperability topics and share your results.
Opportunties for involvement in the CAC by commercial companies also exist, as described at http://nsfcac.org
Know your R usage workflow to handle reproducibility challengesWit Jakuczun
R is used in a vast ways. From pure ad-hoc by hobbysts to an organized and structured way in an enterprise. Each way of R usage brings different reproducibility challenges. Going through range of typical workflows we will show that understanding reproducibility must start with understanding your workflow. Presenting workflows we will show how we deal reproducibiilty challenges with open-source R Suite (http://rsuite.io) solution developed by us to support our large scale R development.
Quick and Dirty: Scaling Out Predictive Models Using Revolution Analytics on ...Revolution Analytics
[Presentation by Skylar Lyon at DataWeek 2014, September 17 2014.]
I recently faced the task of how to scale out an existing analytics process. The schedule was compressed - it always is in my world. The data was big - 400+ million rows waiting in database. What did I do? I offered my favorite type of solution - quick and dirty.
At the outset, I wasn't sure how easy it would be. Nor was I certain of realized performance gains. But the concept seemed sound and the exercise fun. Let's move the compute to the data via Revolution R Enterprise for Teradata.
This presentation outlines my approach in leveraging a colleague's R models as I experimented with running R in-database. Would my path lead to significant improvement? Could it be used to productionalize the workflow?
Massively Scalable Computational Finance with SciDBParadigm4Inc
Hedge funds, investment managers and prop shops need to keep pace with rapidly growing data volumes from many sources.
SciDB—an advanced computational database programmable from R and Python—scales out to petabyte volumes and facilitates rapid integration of diverse data sources. Open source and running on commodity hardware, SciDB is extensible and scales cost effectively.
Attend this webinar to learn how quants and system developers harness SciDB’s massively scalable complex analytics to solve hard problems faster. SciDB’s native array storage is optimized for time-series data, delivering fast windowed aggregates and complex analytics, without time-consuming data extraction.
Webinar presenters will demonstrate real world use cases, including the ability to quickly:
1. Generate aggregated order books across multiple exchanges
2. Create adjusted continuous futures contracts
3. Analyze complex financial networks to detect anomalous behavior
Graph Databases and Machine Learning | November 2018TigerGraph
Graph Database and Machine Learning: Finding a Happy Marriage. Graph Databases and Machine Learning
both represent powerful tools for getting more value from data, learn how they can form a harmonious marriage to up-level machine learning.
Raster Algebra mit Oracle Spatial und uDigKarin Patenge
Im Foliensatz ist die Integration von Oracle Spatial mit Open Source Technolgien beschrieben. Am Beispiel von uDig wird Schritt-für-Schritt aufgezeigt, wie es zusammen mit Oracle Spatial für die Rasterdatenanalyse eingesetzt werden hier. Beispielhaft wird ein Vegetationsindex (NVDI) berechnet.
Bei Interesse gern auch weiterlesen auf dem Oracle Spatial Blog (http://oracle-spatial.blogspot.com).
Bob Jones, CERN & HNSciCloud Coordinator gives an update on the HNSciCloud Pre-Commercial Procurement which is now in its Solution Prototyping phase. The presentation includes also an overview of the prototypes under development.
Full Webinar: https://info.tigergraph.com/graph-gurus-21
In this Graph Gurus episode, we:
Explain the architecture and technical implementation for a TigerGraph + Spark graph-enhanced Machine Learning pipeline
Use TigerGraph both before training to extract (graph and non-graph) features and after training to apply the model on streaming data
Use Spark to train and tune machine learning models at scale
Present a solution in production at China Mobile that detects and prevents phone-based scams using machine learning with TigerGraph
Demo the data flow between Spark and TigerGraph via TigerGraph’s JDBC driver
Sr. Architect Pradeep Reddy, from Qubole, presents the state of Data Science in the enterprise industries today, followed by deep dive of an end-to-end real world machine learning use case. We'll explore the best practices and challenges of big data operations when developing new machine learning features and advanced analytics products at scale in the cloud.
This presentation, given by Bob Jones, CERN & HNSciCloud Coordinator, at the ESA-ESPI Workshop on “Space Data & Cloud Computing Infrastructures: Policies and Regulations”, describes what are the challenges and needs of the cloud users and explains how an hybrid cloud model can support them.
Developing Your Own Flux Packages by David McKay | Head of Developer Relation...InfluxData
Flux is easy to contribute to, and it is easy to share functions and libraries of Flux code with other developers. Although there are many functions in the language, the true power of Flux is its ability to be extended with custom functions. In this session, David will show you how to write your own custom function to perform some new analytics.
SAMOA: A Platform for Mining Big Data Streams (Apache BigData North America 2...Nicolas Kourtellis
A general overview of the APACHE SAMOA platform for mining big data streams using machine learning algorithms running on distributed stream processing platforms such as Apache STORM, Apache Flink, Apache Samza and Apache Apex.
Results are shown from experimentation with VHT, the Vertical Hoeffding Tree proposed in "VHT: Vertical Hoeffding Tree." N. Kourtellis, G. De Francisci Morales, A. Bifet, A. Mordupo. IEEE BigData 2016.
Presentation in APACHE BIG DATA North America 2016
Гостевая лекция Института биоинформатики. Подробнее: http://bioinformaticsinstitute.ru/lectures/1218
Несмотря на несерьезное название, на лекции разговор пойдет о важной проблеме в работе биоинформатика, почти любая реальная задача которого связана с обработкой и анализом больших данных. И решить задачу нужно не только правильно, но и эффективно. Процесс решения можно условно разделить на две части: «придумать», как решать, и «обучить» этому компьютер. И на лекции речь пойдет именно об эффективном «обучении».
Наивно реализованные алгоритмы работают неприемлемо долго, когда дело доходит до гигабайтов реальных данных. От биоинформатика уже требуются не просто базовые навыки программирования, но и знание технических нюансов. И даже у профессионального программиста уйдет немало времени, например, чтобы выгодно использовать возможности Hadoop при работе с Big Data. Так можно ли современному ученому обойтись без тщательного изучения кучи языков, библиотек и фреймворков и сосредоточиться именно на решении?
Are you curious about KNIME Software?
Do you know the difference between KNIME Analytics Platform and KNIME Server?
Which data sources can KNIME connect to?
Can you run an R script from within a KNIME workflow? A Python script? Which other integrations are available?
How can KNIME help with ETL, data preparation, and general data manipulation? Which machine learning algorithms can KNIME offer?
This webinar answers all of these questions! There’s also information about connecting to big data clusters and how you can run the whole or part of your analysis on a big data platform. It also covers everything you need to know about Microsoft Azure and Amazon AWS
KNIME Data Science Learnathon: From Raw Data To Deployment - Paris - November...KNIMESlides
Here are the slides from our Data Science Learnathons. A learnathon is where we learn more about the data science cycle - data access, data blending, data preparation, model training, optimization, testing, and deployment. We also work in groups to hack a workflow-based solution to guided exercises. The tool of choice for this learnathon is KNIME Analytics Platform.
Webinar: Deep Learning Pipelines Beyond the LearningMesosphere Inc.
Mesosphere technical lead Joerg Schad looks at the complete deep learning pipeline. In these slides, Joerg addresses commonly asked questions, such as:
1. How can we easily deploy distributed deep learning frameworks on any public or private infrastructure?
2. How can we manage different deep learning frameworks on a single cluster, especially considering heterogeneous resources such as GPUs?
3. What is the best UI for a data scientist to work with the cluster?
4. How can we store & serve models at scale?
5. How can we update models that are currently in use without causing downtime for the service using them?
6. How can we monitor the entire pipeline and track performance of the deployed models?
This presentation describes some of the Open Source Ai projects we are working at the Center for Open Source, Data and AI Technologies (CODAIT), including Model Asset Exchange (MAX), Fabric for Deep Learning (FfDL) and Jupyter Enterprise Gateway.
H2O Machine Learning with KNIME Analytics Platform - Christian Dietz - H2O AI...Sri Ambati
This talk was recorded in London on October 30, 2018.
KNIME Analytics Platform is an easy to use and comprehensive open source data integration, analysis, and exploration platform, enabling data scientists to visually compose end to end data analysis workflows. The over 2,000 available modules ("nodes") cover each step of the analysis workflow, including blending heterogeneous data types, data transformation, wrangling and cleansing, advanced data visualization, or model training and deployment.
Many of these nodes are provided through open source integrations (why reinvent the wheel?). This provides seamless access to large open source projects such as Keras and Tensorflow for deep learning, Apache Spark for big data processing, Python and R for scripting, and more. These integrations can be used in combination with other KNIME nodes meaning that data scientists can freely select from a vast variety of options when tackling an analysis problem.
The integration of H2O in KNIME offers an extensive number of nodes and encapsulating functionalities of the H2O open source machine learning libraries, making it easy to use H2O algorithms from a KNIME workflow without touching any code - each of the H2O nodes looks and feels just like a normal KNIME node - and the data scientist benefits from the high performance libraries and proven quality of H2O during execution. For prototyping these algorithms are executed locally, however training and deployment can easily be scaled up using a Sparkling Water cluster.
In our talk we give a short introduction to KNIME Analytics Platform and then demonstrate how data scientists benefit from using KNIME Analytics Platform and H2O Machine Learning in combination by using a real world analysis example.
Bio: Christian received a Master’s degree in Computer Science from the University of Konstanz. Having gained experience as a research software engineer at the University of Konstanz, where he developed frameworks and libraries in the fields of bioimage analysis and machine learning, Christian moved on to become a software engineer at KNIME. He now focuses on developing new functionalities and extensions for KNIME Analytics Platform. Some of his recent projects include deep learning integrations built upon Keras and Tensorflow, extensions for image analysis and active learning, and the integration of H2O Machine Learning and H2O Sparkling Water in KNIME Analytics Platform.
Deep learning beyond the learning - Jörg Schad - Codemotion Amsterdam 2018Codemotion
Open Source frameworks such as TensorFlow, MXNet, or PyTorch enable anyone to model and train Deep Neural Networks. While there are many great tutorials and talks showing us the best ways for training models, there is few information on what happens after we have trained our model? How can we store, utilize, and update it? In this talk, we look at the complete Deep Learning Pipeline and looks at topics such as deployments, multi-tenancy, jupyter notebooks, model serving, and more.
If you understand the rule engine, especially how works RETE algorithm, You may use this for Machine Learning. This slide used at Red Hat Forum Tokyo 2018 session.
In March and April 2018 KNIME hosted a series of Learnathons in the US. You can find the slides that were presented here.
For more upcoming events and courses visit: https://www.knime.com/learning/events
Inteligencia artificial, open source e IBM Call for CodeLuciano Resende
Nesta palestra vamos abordar algumas das tendências em Inteligência Artificial e as dificuldades na uso da Inteligência Artificial. Por isso, também apresentaremos algumas ferramentas disponíveis em código livre que podem ajudar a simplificar a adoção da IA. E faremos uma breve introdução ao “Call for Code” que é uma iniciativa da IBM para construir soluções na prevenção e reação a desastres naturais.
Charles sonigo - Demuxed 2018 - How to be data-driven when you aren't Netflix...Charles Sonigo
How can you improve complex video software when your performance indicators are highly variable? The answer is proper methodology, proper data infrastructure and analysis.
Curated "Cloud Design Patterns" for Call Center PlatformsAlejandro Rios Peña
As presented at Opensips Summit May 1st 2018, Amsterdam.
When designing cloud-based contact center solutions there are many challenges to overcome, and many roads to success. Most cloud-architects have encountered these problems before, and have used common solutions to remedy them. If you encounter these problems, why recreate a solution when you can use an already proven answer? Cloud Design Patterns (CDP) are solutions and design ideas for using cloud technology to solve common platform design problems.
Kamanja: Driving Business Value through Real-Time Decisioning SolutionsGreg Makowski
This is a first presentation of Kamanja, a new open-source real-time software product, which integrates with other big-data systems. See also links: http://www.meetup.com/SF-Bay-ACM/events/223615901/ and http://Kamanja.org to download, for docs or community support. For the YouTube video, see https://www.youtube.com/watch?v=g9d87rvcSNk (you may want to start at minute 33).
What's New in KNIME Analytics Platform 4.1KNIMESlides
Slides from our recent webinar highlighting the newest features in KNIME Analytics Platform 4.1 and KNIME Server 4.10
It covers all the new features like Guided Labeling and all the new nodes such as the Binary Classification Inspector node, and WebRetriever node. It covers public and private spaces on the KNIME Hub and how the Hub can help you build your workflows more quickly and easily by giving you access to components. It also covers the additional cloud connectivity as well as the new Create Databricks Environment node for connecting to your Databricks cluster running on Microsoft Azure or Amazon AWS.
On the KNIME Server side, we highlight how the server now supports the open standard for authorization - OAuth identification as well as how you can more easily configure workflows that are already running on KNIME Server.
View the webinar here: https://www.youtube.com/watch?v=VzNqE4WklEk
Read here for more details on this release: https://www.knime.com/whats-new-in-knime-41
Workshop 1. Architecting Innovative Graph Applications
Join this hands-on workshop for beginners led by Neo4j experts guiding you to systematically uncover contextual intelligence. Using a real-life dataset we will build step-by-step a graph solution; from building the graph data model to running queries and data visualization. The approach will be applicable across multiple use cases and industries.
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.
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.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
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.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.