Bioinformatics Databases
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Bioinformatics databases aim to manage the complexity of life by integrating diverse biological data types. Relational databases use standardized identifiers and data formats to store sequence, expression, proteomic, and metabolomic data. Cross-referencing multiple databases through data warehousing and centralized schemas allows for functional querying of biological networks and neighborhoods. Future directions include greater use of machine learning, data mining, and global data standards.
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INTRODUCTION
HISTORY
WHAT ARE THE DATABASE…?
WHY DATABASE….?
THE “PERFECT” DATABASE
IDENTIFIERS and ACCESSION NUMBER
TECHNICAL DESIGN
MAINTAINANCE OF BIOLOGICAL DATABASES..
GENERAL FEATURES
SOURCES OF BIOLOGICAL DATA…
DIFFERENT TYPES OF BIOLOGICAL DATABASE
FUNCTION
DATA ENTRY AND QUALITY CONTROL
AVAILIBILITY
APPLICATION
DATA RECORD AT THE YEAR 2004
CONCLUSION
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PRIMARY DATABASE
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Biological database by kk sahu
INTRODUCTION
HISTORY
WHAT ARE THE DATABASE…?
WHY DATABASE….?
THE “PERFECT” DATABASE
IDENTIFIERS and ACCESSION NUMBER
TECHNICAL DESIGN
MAINTAINANCE OF BIOLOGICAL DATABASES..
GENERAL FEATURES
SOURCES OF BIOLOGICAL DATA…
DIFFERENT TYPES OF BIOLOGICAL DATABASE
FUNCTION
DATA ENTRY AND QUALITY CONTROL
AVAILIBILITY
APPLICATION
DATA RECORD AT THE YEAR 2004
CONCLUSION
REFFERENCES
Bioinformatics principles and applications
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This document provides an overview of bioinformatics and bioinformatics databases. It defines bioinformatics as the application of information technology to molecular biology to analyze and interpret biological data. This includes tasks like mapping and analyzing DNA and protein sequences. The document discusses how bioinformatics databases are used to store and manage the large amounts of biological data generated. It describes the characteristics of biological databases and how they are used for querying and retrieving sequence information. Key areas of bioinformatics research and important sequence databases are also summarized.Primary and secondary database
INTRODUCTION
WHAT IS DATA AND DATABASE?
WHAT IS BIOLOGICAL DATABASE?
TYPES OF BIOLOGICAL DATABASE
PRIMARY DATABASE
Nucleic acid sequence database
Protein sequence database
SECONDARY DATABASE
COMPOSITE DATABASE
TERTIARY DATABASE
WHY NEED?
CONCLUSION
REFRENCES
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Data acquisition
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Principal Component Analysis
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This document discusses biological databases. It begins by defining what a database is and describing database architecture. It then discusses several major types of biological databases including nucleotide sequence databases like GenBank, protein sequence databases like PDB, and collaborative databases. Specific databases discussed in detail include GenBank, NCBI, DDBJ, Swiss-Prot, TrEMBL, and UniProt. The document explains the purpose and contributions of these different biological databases.
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This document discusses biological databases. It defines a biological database as a collection of structured, searchable, and periodically updated biological data like protein sequences, molecular structures, and DNA sequences. It notes that biological data is heterogeneous, high-volume, uncertain, dynamically changing, and integrated from various global sources. The key functions of biological databases are to make biological data available worldwide in a computer-readable format. They are broadly classified into sequence, structure, and pathway databases. Some examples of important biological databases discussed are Swiss-Prot, PDB, GenBank, and COGs.
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Biological database
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LECTURE NOTES ON BIOINFORMATICS
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
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The EMBL Australian Bioinformatics Resource (EMBL-ABR) is a distributed national research infrastructure that provides bioinformatics support to life science researchers in Australia. It has a hub-and-nodes structure with the hub hosted at the Victorian Life Science Computation Initiative at the University of Melbourne and 10 nodes located across Australian institutions. EMBL-ABR aims to increase Australia's capacity for bioinformatics research and data science, provide training in bioinformatics, and enable participation in international collaborations.
FAIRy Stories
Findable Accessable Interoperable Reusable < data |models | SOPs | samples | articles| * >. FAIR is a mantra; a meme; a myth; a mystery; a moan. For the past 15 years I have been working on FAIR in a bunch of projects and initiatives in Life Science projects. Some are top-down like Life Science European Research Infrastructures ELIXIR and ISBE, and some are bottom-up, supporting research projects in Systems and Synthetic Biology (FAIRDOM), Biodiversity (BioVel), and Pharmacology (open PHACTS), for example. Some have become movements, like Bioschemas, the Common Workflow Language and Research Objects. Others focus on cross-cutting approaches in reproducibility, computational workflows, metadata representation and scholarly sharing & publication. In this talk I will relate a series of FAIRy tales. Some of them are Grimm. Some have happy endings. Who are the villains and who are the heroes? What are the morals we can draw from these stories?
Research data and scholarly publications: going from casual acquaintances to ...
Presented to ALPSP annual meeting 2011 in Oxfordshire UK during a session entitled "Abort Retry Fail? Data and the scholarly literature"
Research Objects: more than the sum of the parts
Workshop on Managing Digital Research Objects in an Expanding Science Ecosystem, 15 Nov 2017, Bethesda, USA
https://www.rd-alliance.org/managing-digital-research-objects-expanding-science-ecosystem
Research output is more than just the rhetorical narrative. The experimental methods, computational codes, data, algorithms, workflows, Standard Operating Procedures, samples and so on are the objects of research that enable reuse and reproduction of scientific experiments, and they too need to be examined and exchanged as research knowledge.
A first step is to think of Digital Research Objects as a broadening out to embrace these artefacts or assets of research. The next is to recognise that investigations use multiple, interlinked, evolving artefacts. Multiple datasets and multiple models support a study; each model is associated with datasets for construction, validation and prediction; an analytic pipeline has multiple codes and may be made up of nested sub-pipelines, and so on. Research Objects (http://researchobject.org/) is a framework by which the many, nested and contributed components of research can be packaged together in a systematic way, and their context, provenance and relationships richly described.
Big Data Repository for Structural Biology: Challenges and Opportunities by P...
SBGrid (Morin et al., 2013, eLIFE and www.sbgrid.org) is a Harvard based structural biology global computing consortium with a primary focus on the curation of research software. Dr. Sliz will discuss a recent SBGrid project that aims to establish a repository for experimental datasets from SBGrid laboratories. Issues of handling large data volumes, data validation and repository sustainability will be addressed in this talk.
Knowledge Exchange, Nov 2011, Bonn
Keynote presented to KE workshop held in conjunction with the release of the report "A Surfboard for Riding the Wave
Towards a four country action programme on research data": http://www.knowledge-exchange.info/Default.aspx?ID=469
Data Infrastructure for Coastal and Estuarine Science
This talk was given at the Atlantic Estuarine Research Society at their 2014 Sprint meeting in Ocean City, Maryland, USA
Enriching Scholarship 2014 Beyond the Journal Article: Publishing and Citing ...
The document discusses data sharing policies and mandates from various organizations including federal funding agencies in the US and internationally, journals, and a paradigm shift toward more transparent and collaborative research that integrates publications and data. Key points include requirements for data management plans from NIH and NSF, expectations of funding agencies in other countries to maximize access to research data, a journal policy requiring data to be made available, and challenges around measuring the impact of shared data given the lack of common practices and standards for citing data.
VIVO: enabling the discovery of research and scholarship
An introduction to VIVO, an open source, semantic web application that enables discovery of research and scholarship across institutions and one library's role in its implementation and development.
Curation and Preservation of Crystallography Data
A presentation given by Manjula Patel (UKOLN) at "Chemistry in the Digital Age: A Workshop connecting research and education", June 11-12th 2009, Penn State University,
http://www.chem.psu.edu/cyberworkshop09
CTSA Inventory Resource Web Presence
The document describes the CTSA Inventory Resource Web Presence (CIRWP), a web-accessible and searchable inventory of research resources across the CTSA consortium. It outlines the development of CIRWP, including building an informatics infrastructure based on standards, extending ontologies to annotate resource descriptions, and deploying web services and tools to enable a distributed inventory. CIRWP includes full or partial inventories from 37 CTSA sites cataloging over 370 informatics resources. The document discusses future goals of CIRWP such as accelerating harmonization across organizations and outreach, and highlights evaluations conducted to design CIRWP with user-centered approaches.
Being FAIR: Enabling Reproducible Data Science
Talk presented at Early Detection of Cancer Conference, OHSU, Portland, Oregon USA, 2-4 Oct 2018, http://earlydetectionresearch.com/ in the Data Science session
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NY Prostate Cancer Conference - P.A. Fearn - Session 1: Data management for p...
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Research data and scholarly publications: going from casual acquaintances to ...
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Recently uploaded
Uni Systems Copilot event_05062024_C.Vlachos.pdf
Unlocking Productivity: Leveraging the Potential of Copilot in Microsoft 365, a presentation by Christoforos Vlachos, Senior Solutions Manager – Modern Workplace, Uni Systems
Presentation of the OECD Artificial Intelligence Review of Germany
Consult the full report at https://www.oecd.org/digital/oecd-artificial-intelligence-review-of-germany-609808d6-en.htm
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slack
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
Artificial Intelligence for XMLDevelopment
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
OpenID AuthZEN Interop Read Out - Authorization
During Identiverse 2024 and EIC 2024, members of the OpenID AuthZEN WG got together and demoed their authorization endpoints conforming to the AuthZEN API
20240607 QFM018 Elixir Reading List May 2024
Everything I found interesting about the Elixir programming ecosystem in May 2024
Your One-Stop Shop for Python Success: Top 10 US Python Development Providers
Simplify your search for a reliable Python development partner! This list presents the top 10 trusted US providers offering comprehensive Python development services, ensuring your project's success from conception to completion.
Programming Foundation Models with DSPy - Meetup Slides
Prompting language models is hard, while programming language models is easy. In this talk, I will discuss the state-of-the-art framework DSPy for programming foundation models with its powerful optimizers and runtime constraint system.
“Building and Scaling AI Applications with the Nx AI Manager,” a Presentation...
“Building and Scaling AI Applications with the Nx AI Manager,” a Presentation...Edge AI and Vision Alliance
For the full video of this presentation, please visit: https://www.edge-ai-vision.com/2024/06/building-and-scaling-ai-applications-with-the-nx-ai-manager-a-presentation-from-network-optix/
Robin van Emden, Senior Director of Data Science at Network Optix, presents the “Building and Scaling AI Applications with the Nx AI Manager,” tutorial at the May 2024 Embedded Vision Summit.
In this presentation, van Emden covers the basics of scaling edge AI solutions using the Nx tool kit. He emphasizes the process of developing AI models and deploying them globally. He also showcases the conversion of AI models and the creation of effective edge AI pipelines, with a focus on pre-processing, model conversion, selecting the appropriate inference engine for the target hardware and post-processing.
van Emden shows how Nx can simplify the developer’s life and facilitate a rapid transition from concept to production-ready applications.He provides valuable insights into developing scalable and efficient edge AI solutions, with a strong focus on practical implementation.National Security Agency - NSA mobile device best practices
Threats to mobile devices are more prevalent and increasing in scope and complexity. Users of mobile devices desire to take full advantage of the features
available on those devices, but many of the features provide convenience and capability but sacrifice security. This best practices guide outlines steps the users can take to better protect personal devices and information.
GraphRAG for Life Science to increase LLM accuracy
GraphRAG for life science domain, where you retriever information from biomedical knowledge graphs using LLMs to increase the accuracy and performance of generated answers
CAKE: Sharing Slices of Confidential Data on Blockchain
Presented at the CAiSE 2024 Forum, Intelligent Information Systems, June 6th, Limassol, Cyprus.
Synopsis: Cooperative information systems typically involve various entities in a collaborative process within a distributed environment. Blockchain technology offers a mechanism for automating such processes, even when only partial trust exists among participants. The data stored on the blockchain is replicated across all nodes in the network, ensuring accessibility to all participants. While this aspect facilitates traceability, integrity, and persistence, it poses challenges for adopting public blockchains in enterprise settings due to confidentiality issues. In this paper, we present a software tool named Control Access via Key Encryption (CAKE), designed to ensure data confidentiality in scenarios involving public blockchains. After outlining its core components and functionalities, we showcase the application of CAKE in the context of a real-world cyber-security project within the logistics domain.
Paper: https://doi.org/10.1007/978-3-031-61000-4_16
Removing Uninteresting Bytes in Software Fuzzing
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
Columbus Data & Analytics Wednesdays - June 2024
Columbus Data & Analytics Wednesdays, June 2024 with Maria Copot 20
HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAU
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-und-domino-lizenzkostenreduzierung-in-der-welt-von-dlau/
DLAU und die Lizenzen nach dem CCB- und CCX-Modell sind für viele in der HCL-Community seit letztem Jahr ein heißes Thema. Als Notes- oder Domino-Kunde haben Sie vielleicht mit unerwartet hohen Benutzerzahlen und Lizenzgebühren zu kämpfen. Sie fragen sich vielleicht, wie diese neue Art der Lizenzierung funktioniert und welchen Nutzen sie Ihnen bringt. Vor allem wollen Sie sicherlich Ihr Budget einhalten und Kosten sparen, wo immer möglich. Das verstehen wir und wir möchten Ihnen dabei helfen!
Wir erklären Ihnen, wie Sie häufige Konfigurationsprobleme lösen können, die dazu führen können, dass mehr Benutzer gezählt werden als nötig, und wie Sie überflüssige oder ungenutzte Konten identifizieren und entfernen können, um Geld zu sparen. Es gibt auch einige Ansätze, die zu unnötigen Ausgaben führen können, z. B. wenn ein Personendokument anstelle eines Mail-Ins für geteilte Mailboxen verwendet wird. Wir zeigen Ihnen solche Fälle und deren Lösungen. Und natürlich erklären wir Ihnen das neue Lizenzmodell.
Nehmen Sie an diesem Webinar teil, bei dem HCL-Ambassador Marc Thomas und Gastredner Franz Walder Ihnen diese neue Welt näherbringen. Es vermittelt Ihnen die Tools und das Know-how, um den Überblick zu bewahren. Sie werden in der Lage sein, Ihre Kosten durch eine optimierte Domino-Konfiguration zu reduzieren und auch in Zukunft gering zu halten.
Diese Themen werden behandelt
- Reduzierung der Lizenzkosten durch Auffinden und Beheben von Fehlkonfigurationen und überflüssigen Konten
- Wie funktionieren CCB- und CCX-Lizenzen wirklich?
- Verstehen des DLAU-Tools und wie man es am besten nutzt
- Tipps für häufige Problembereiche, wie z. B. Team-Postfächer, Funktions-/Testbenutzer usw.
- Praxisbeispiele und Best Practices zum sofortigen Umsetzen
“I’m still / I’m still / Chaining from the Block”
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
Full-RAG: A modern architecture for hyper-personalization
Mike Del Balso, CEO & Co-Founder at Tecton, presents "Full RAG," a novel approach to AI recommendation systems, aiming to push beyond the limitations of traditional models through a deep integration of contextual insights and real-time data, leveraging the Retrieval-Augmented Generation architecture. This talk will outline Full RAG's potential to significantly enhance personalization, address engineering challenges such as data management and model training, and introduce data enrichment with reranking as a key solution. Attendees will gain crucial insights into the importance of hyperpersonalization in AI, the capabilities of Full RAG for advanced personalization, and strategies for managing complex data integrations for deploying cutting-edge AI solutions.
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Presentation of the OECD Artificial Intelligence Review of Germany
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Your One-Stop Shop for Python Success: Top 10 US Python Development Providers
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Programming Foundation Models with DSPy - Meetup Slides
Programming Foundation Models with DSPy - Meetup Slides
“Building and Scaling AI Applications with the Nx AI Manager,” a Presentation...
“Building and Scaling AI Applications with the Nx AI Manager,” a Presentation...
National Security Agency - NSA mobile device best practices
National Security Agency - NSA mobile device best practices
GraphRAG for Life Science to increase LLM accuracy
GraphRAG for Life Science to increase LLM accuracy
CAKE: Sharing Slices of Confidential Data on Blockchain
CAKE: Sharing Slices of Confidential Data on Blockchain
HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAU
HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAU
Full-RAG: A modern architecture for hyper-personalization
Full-RAG: A modern architecture for hyper-personalization
Bioinformatics Databases
- 1. BIOINFORMATICS DATABASES: MANAGING THE COMPLEXITY OF LIFE Christopher Schlosberg CS 411 Graduate Project
- 3. Protein Sequence Search [12]
- 5. General Bio-DB Development Considerations [11] [2]
- 8. SQL Implementation for Feeder DBs [9]