Chemoinformatics involves the management and analysis of chemical structure data to help accelerate the drug discovery process. It uses computer representations of molecules and applies techniques like database searching, fingerprinting, and molecular modeling to efficiently screen large numbers of chemical structures. This helps identify potential drug leads and reject non-drug candidates more quickly compared to traditional sequential drug screening. Key applications of chemoinformatics include structure and substructure searching of databases, molecular similarity analysis and virtual screening to predict molecular properties and activity.
Digital interface has transformed branding. This keynote presentation discusses how to brand your products and services in this paradigm-changing media.
Digital interface has transformed branding. This keynote presentation discusses how to brand your products and services in this paradigm-changing media.
DWPI Markush Database on STN – A New Perspective for Searching Markush Struct...Dr. Haxel Consult
Searching for Markush structures has been a rather difficult task especially since it was necessary in the past to work with different retrieval systems. With the new implementation of the DWPI Markush database from Thomson Reuters on STN it is now possible to search for Markush structures using a single structure query for all structure databases. In this system the structure and bibliographic databases are integrated within a content domain which allows easy and fast projections between the databases. It will be shown that the DWPI Markush concept of superatoms can be integrated in the STN query system, allowing users to exploit the full potential of the DWPI Markush data. To enable complete and high precision searches it was necessary to develop a new Markush search engine. Improved evaluation of Markush structures is possible with hit structure display, highlighting, and assembled structures. Based on this implementation it will be possible to develop further innovative features in the future.
Applied Bioinformatics & Chemoinformatics: Techniques, Tools, and OpportunitiesHezekiah Fatoki
The computational methods for in silico drug discovery have been broadly categories into two fields bioinformatics and chemoinformatics. In case of bioinformatics, major emphasis is on identification and validation of drug targets, mainly based on functional/structural annotation of genomes. In case of chemoinformatics or pharmacoinformatics, major emphasis is on designing of drug molecules or ligands and their interaction with drug targets.
Naked DNA And DNA Vaccines A Retrospectiverwmalonemd
A retrospective review starting from the genesis of genetic vaccination and naked gene delivery through development of cationic lipid and electroporative delivery of DNA (skin, muscle, liver, lung)
DWPI Markush Database on STN – A New Perspective for Searching Markush Struct...Dr. Haxel Consult
Searching for Markush structures has been a rather difficult task especially since it was necessary in the past to work with different retrieval systems. With the new implementation of the DWPI Markush database from Thomson Reuters on STN it is now possible to search for Markush structures using a single structure query for all structure databases. In this system the structure and bibliographic databases are integrated within a content domain which allows easy and fast projections between the databases. It will be shown that the DWPI Markush concept of superatoms can be integrated in the STN query system, allowing users to exploit the full potential of the DWPI Markush data. To enable complete and high precision searches it was necessary to develop a new Markush search engine. Improved evaluation of Markush structures is possible with hit structure display, highlighting, and assembled structures. Based on this implementation it will be possible to develop further innovative features in the future.
Applied Bioinformatics & Chemoinformatics: Techniques, Tools, and OpportunitiesHezekiah Fatoki
The computational methods for in silico drug discovery have been broadly categories into two fields bioinformatics and chemoinformatics. In case of bioinformatics, major emphasis is on identification and validation of drug targets, mainly based on functional/structural annotation of genomes. In case of chemoinformatics or pharmacoinformatics, major emphasis is on designing of drug molecules or ligands and their interaction with drug targets.
Naked DNA And DNA Vaccines A Retrospectiverwmalonemd
A retrospective review starting from the genesis of genetic vaccination and naked gene delivery through development of cationic lipid and electroporative delivery of DNA (skin, muscle, liver, lung)
Wikipedia at the Royal Society: The Good, the Bad and the UglyDuncan Hull
Wikipedia has a troubled relationship with scientists and their science. Many scientists are wary of editing Wikipedia and reluctant to contribute their knowledge to it, despite its global reach. Consequently, Wikipedia's coverage of Science is very variable with many notable scientists work either completely absent or poorly described.
There are several WikiProjects that are tackling these problems across Science, including in Computational Biology, Medicine, Cell Biology, Physiology and Women Scientists.
This talk will describe how the WikiProject Royal Society has addressed these issues, through its Wikipedian in Residence scheme. We will examine the outcomes of the project as well as the challenges that remain for this ongoing collaboration between the Royal Society and Wikimedia UK.
We will discuss the good, bad and "ugly" aspects of scientists Wiki-biographies (quick biographies in Wikipedia) and draw conclusions about improving coverage of Scientists, and their Science in Wikipedia using the resources of a learned academic society.
Speaker biography: Dr. Duncan Hull is a lecturer in the School of Computer Science at the University of Manchester who started editing Wikipedia in 2004. He helped setup the Wikipedian in Residence scheme at the Royal Society in 2012.
Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome CampusDuncan Hull
Abstract: This talk will describe the use of http://www.citeulike.org to manage and share bibliographic references among 1300 scientists and engineers working at the Sanger Institute (http://www.sanger.ac.uk) and European Bioinformatics Insitute (http://www.ebi.ac.uk) based on the Wellcome Trust Genome Campus in Cambridge, UK. Using data from references shared so far, we will illustrate the costs, benefits and adoption of citeulike to create and share bibliographic data on the web.
Presentation from The Influence and Impact of Web 2.0 on Various Applications at the National e-Science Centre, Edinburgh, UK.
Part of a joint presentation with Midori Harris comparing OWL (Web Ontology Language) and OBO (Open Biomedical Ontologies) as ontology languages, This presentation concentrates on OWL, Midori Harris presented OBO.
Accessing small molecule data using ChEBIDuncan Hull
Presentation on Chemical Entities of Biological Interest (ChEBI) for the Programmatic Access to Biological Databases (Perl) course
22-26 February 2010 @ EBI
Slides from the "Author Identity – Creating a new kind of reputation online" session at Science Online London (solo09) with Duncan Hull, Geoffrey Bilder, Michael Habib, Reynold Guida
ResearcherID, Contributor ID, Scopus Author ID, etc. help to connect your scientific record. How do these tools connect to your online identity, and how can OpenID and other tools be integrated? How can we build an online reputation and when should we worry about our privacy?
Digital Identity is fundamental to collaboration in bioinformatics research and development because it enables attribution, contribution, publication to be recorded and quantified.
However, current models of identity are often obsolete and have problems capturing both small contributions "microattribution" and large contributions "mega-attribution" in Science. Without adequate identity mechanisms, the incentive for collaboration can be reduced, and the utility of collaborative social tools hindered.
Using examples of metabolic pathway analysis with the taverna workbench and myexperiment.org, this talk will illustrate problems and solutions to identifying scientists accurately and effectively in collaborative bioinformatics networks on the Web.
The Year of Blogging Dangerously: Lessons from the "Blogosphere". This talk will describe how to build an institutional repository using free (or cheap) web-based and blogging tools including flickr.com, slideshare.net, citeulike.org, wordpress.com, myexperiment.org and friendfeed.com. We will discuss some strengths and limitations of these tools and what Institutional Repositories can learn from them.
Defrosting the Digital Library: A survey of bibliographic tools for the next ...Duncan Hull
After centuries with little change, scientific libraries have recently experienced massive upheaval. From being almost entirely paper-based, most libraries are now almost completely digital. This information revolution has all happened in less than 20 years and has created many novel opportunities and threats for scientists, publishers and libraries.
Today, we are struggling with an embarassing wealth of digital knowledge on the Web. Most scientists access this knowledge through some kind of digital library, however these places can be cold, impersonal, isolated, and inaccessible places. Many libraries are still clinging to obsolete models of identity, attribution, contribution, citation and publication.
Based on a review published in PLoS Computational Biology, http://pubmed.gov/18974831 this talk will discuss the current chilly state of digital libraries for biologists, chemists and informaticians, including PubMed and Google Scholar. We highlight problems and solutions to the coupling and decoupling of publication data and metadata, with a tool called http://www.citeulike.org. This software tool exploits the Web to make digital libraries “warmer”: more personal, sociable, integrated, and accessible places.
Finally issues that will help or hinder the continued warming of libraries in the future, particularly the accurate identity of authors and their publications, are briefly introduced. These are discussed in the context of the BBSRC funded REFINE project, at the National Centre for Text Mining (NaCTeM.ac.uk), which is linking biochemical pathway data with evidence for pathways from the PubMed database.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
• The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
• Test Automation: How AI-powered test case generation, optimization, and self-healing tests are making testing more efficient and effective.
• Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
• Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
PHP Frameworks: I want to break free (IPC Berlin 2024)Ralf Eggert
In this presentation, we examine the challenges and limitations of relying too heavily on PHP frameworks in web development. We discuss the history of PHP and its frameworks to understand how this dependence has evolved. The focus will be on providing concrete tips and strategies to reduce reliance on these frameworks, based on real-world examples and practical considerations. The goal is to equip developers with the skills and knowledge to create more flexible and future-proof web applications. We'll explore the importance of maintaining autonomy in a rapidly changing tech landscape and how to make informed decisions in PHP development.
This talk is aimed at encouraging a more independent approach to using PHP frameworks, moving towards a more flexible and future-proof approach to PHP development.
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
2. Overview
• What is chemoinformatics and why is it
necessary
• Managing structural information
• Typical facilities in chemoinformatics
software
• Examples of current research
3. Drug discovery: I
• Drug discovery is a vastly complex, multi-disciplinary
task that can extend over two decades
• The total cost for the discovery and development of a
novel therapeutic agent is now ca. $1.5B
• Even so, only about 1 in 3 cover the R&D costs
• But when they can do the pay-offs can be massive: Lipitor in
2006 made $12.5B (cf MS Windows and Boeing 747)
• Patent cover is 20 years from initial announcement
• Time is money so need to find potential drugs (and to reject non-
drugs) much faster (and similarly for agrochemicals)
4. Drug discovery: II
• Chemoinformatics is one way of increasing the cost
effectiveness of drug discovery
• Initial work in chemoinformatics as early as the Sixties:
current interest because of developments in
• Combinatorial chemistry
• High throughput screening (HTS)
• Change from sequential to massively parallel processing
• Resulting explosion in the amounts of data available in
drug-discovery programmes, and an increased interest
in computational methods
• Focus on chemical structure diagram, cf development of other
types of -informatics specialisms
5. Definitions
• F.K. Brown (1998). Annual Reports in Medicinal Chemistry, 33,
375-384
• “The use of information technology and management has become
a critical part of the drug discovery process. Chemoinformatics is
the mixing of those information resources to transform data into
information and information into knowledge for the intended
purpose of making better decisions faster in the area of drug lead
identification and optimization”
• G. Paris (August 1999 ACS meeting), quoted by W.A. Warr at
http://www.warr.com/warrzone.htm
• “Chem(o)informatics is a generic term that encompasses the
design, creation, organization, management, retrieval, analysis,
dissemination, visualization and use of chemical information”
• J. Gasteiger and T. Engels (editors) (2003). Chemoinformatics:
a textbook. Wiley-VCH.
• “Chemoinformatics is the application of informatics methods to
solve chemical problems.”
6. Representation of molecules
• Need for a machine-readable representation
• 1D – computed/experimental global properties
• 2D – the chemical structure diagram
• 3D – atomic coordinate data
• 1D representations handled using conventional
DBMS software
• Need to manipulate 2D and 3D data
7. Connection tables
9 1 C 2 2 6 1 7 1
O 2 C 1 2 3 1
2 3 C 2 1 4 2
1
3 4 C 3 2 5 1
7
8 5 C 4 1 6 2
4 6 C 1 1 5 2
6
7 C 1 1 8 1 9 2
5 8 C 7 1
9 O 7 2
• An unambiguous representation of a 2D chemical
structure diagram
• A connection table is a graph, the underlying data
structure in chemoinformatics
8. Graph theory and chemistry
• Graph theory
• Branch of mathematics that describes sets of objects, called
nodes and the relationships between them, called edges
O
• A 2D connection table is a graph: Br
• Nodes correspond to atoms
• Edges correspond to bonds
NH 2
• Graph matching algorithms
• Search chemical databases
• Generation of other representations
9. Types of search
• Exact structure search (hashed connection table with
graph isomorphism for collision handling)
• Substructure search (subgraph isomorphism)
• cf partial or boolean matching in text
• Similarity searching (maximal common subgraph
isomorphism (or simpler))
• cf best match search or web searching
• Graph matching algorithms are effective
• But time is factorial with the number of nodes
• Need for efficient heuristics
10. Fingerprints C
O
C C C
C C C
C
• A fingerprint (or fragment bit-string) is a binary vector
encoding the presence (“1”) or absence (“0”) of
fragment substructures in a molecule
• Each bit in the fingerprint represents one molecular
fragment. Typical length is ~1000 bits
• An approximate representation, but one that can be
processed very efficiently and hence often used as a
precursor to graph matching
11. Chemoinformatics facilities
• Database searching as described previously
• Structure and substructure searching originally
• Similarity searching from mid-Eighties
• 3D substructure searching from mid-Nineties (first rigid then
flexible)
• Applications
• Database clustering
• Molecular diversity analysis
• Drug-likeness
• Virtual screening
Ligand-based
Structure-based
12. 3D substructure
searching
• Generation of pharmacophore patterns
• Use of MOGA and hyperstructure approaches
O a = 8.62+ 0.58 Angstroms
- N
O
b = 7.08+ 0.56 Angstroms
-
c a c = 3.35+ 0.65 Angstroms O
-
O O
b N O O
O
S
N
O N
O
O O N
O N
N
O
O O
N N N O
O O O P O O
N O N
N
O N O P O
O N O
O N
N O P O
O
O O O
N O O
O O
13. Similarity searching
using 2D fingerprints
Use of data fusion methods to enhance performance,
combining information from multiple searches
H
N O
H H H2N
N N OH H
N N NH2 N
N
Q uery
N
N
OH
H H2N
HO N
N
H N
N N
N
14. Molecular modelling and QSAR
• Use of computational chemistry to obtain the structures
and properties of small molecules
• Quantum mechanics
• Molecular dynamics
• Molecular modelling
• Statistical correlation of structure (however described)
with physical, chemical and biological properties
• Initially biological activity (QSAR)
• Now pharmacokinetics and toxicity (ADMET)
15. Integration with database searching
• Related, but largely separate, research areas for many
years
• Simple search operations on very large numbers of molecules
• Increasingly complex operations on smaller and smaller
(normally homogeneous) datasets
• Substructural analysis as an early, notable exception
• The future lies in the integration of these two
approaches, applying more sophisticated methods on
larger datasets
• Docking now well established
• Property calculations at a database level
• ADMET
16. General references
J. Gasteiger (ed.), Handbook of Chemoinformatics (Wiley-VCH,
Weinheim, 2003).
W.L. Chen, Chemoinformatics: past, present and future, Journal of
Chemical Information and Modeling 46 (2006) 2230-2255.
D.J. Wild and G.D. Wiggins, Challenges for chemoinformatics
education in drug discovery, Drug Discovery Today 11 (2006) 436-
439.
A.R. Leach and V.J. Gillet, An Introduction to Chemoinformatics
(Kluwer, Dordrecht, 2nd sedition, 2007).
P. Willett, A bibliometric analysis of chemoinformatics, Aslib
Proceedings 60 (2008) 4-17.