EUGM 2014 - Eufrozina Hoffmann (ChemAxon): Smart Drawing with Marvin JS

•

1 j'aime•330 vues

In the last two years, we transitioned the most-asked-for features from our successful MarvinSketch desktop application to a new lightweight web component: Marvin JS. However this was not a simple copy/pasting of features. The challenges of JavaScript technology, the possibilities of touch screen drawing and the benefits of hindsight made us re-imagine even the most basic drawing features to create a clean, straight forward user-oriented tool.

Smart Drawing with Marvin JS
Efi Hoffmann

Marvin: Drawing&Displaying
Marvin for JavaScriptMarvin AppletMarvin Beans
Web
Desktop & Server
Java JavaScript

Marvin JS
• lightweight web component -> Architecture
JavaScript, Html5, CSS3
• only a browser is needed to run
• easy to integrate
• fast startup, fast download
• ready for tablets
Client ServerMRV
Web ServiceMarvin JS

New techniques Features
Challenge
Opportunity

5
Reactions

6
R-groups

7
Electron flow arrows

8
GUI Presets

Coming soon... (6.4)
• Custom templates (server side)
• Basic 3D & display options
9

Future plans
More query feature:
-reaction query
-query atomic properties
-link node
...
10

Thank you for your attention!

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Marvin JS is a novel light-weight chemical editor suitable for generating standard chemical structures without the need for installing Java, designed by ChemAxon. It provides all the essential features for quick and easy structure drawing as well as flexible editing options for molecular manipulations. Pearson Education is partnering with ChemAxon to develop a custom educational version of Marvin JS to be used in Pearson’s chemical tutorial platform, MasteringChemistry. This educational version of Marvin JS separates out various tools into “presets” to match specific answer types that Pearson authors have designed – skeletal 2D problems, skeletal 3D problems and mechanism problems. For example, tools necessary for drawing mechanisms will only be available for those problems that ask the student to draw a mechanism. In additional, authors will be able to set specific initialization parameters for individual problems such as “show lone pairs” or “show R,S labels”. This higher level of feature control allows authors to better regulate what students are able to see and able to do in the drawing tool, minimizing opportunities for mistakes (using the wrong templates for example) or cheating (using R,S labels to answer a stereochemistry question). Pearson will offer this custom version of Marvin JS for Organic and General Chemistry drawing items both for desktop and for mobile beginning in January 2014.

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Marvin JS is the newest member of the Marvin product family. The chemical smartness of MarvinSketch has been transferred to this clean, straight-forward, user-oriented web component. This transfer does not mean that developing Marvin JS was a simple copy/paste of features. The extensive potential in the JavaScript technology, especially its adoptability on touch devices, drove us to re-imagine even the most basic drawing features. During the development we tried to find the balance between the robust chemical knowledge and the intuitive usage.

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With the addition of a molecular similarity search capability, the ChemAxon Markush Search platform is now capable of performing Exact, Sub-Structure, and Similarity searches. Those three types of searches are commonly used by drug discovery chemists to search against molecular databases containing up to 109 molecules. This effectively places very large (1012 – 1018) chemical compound spaces, real or virtual, which can be expressed as Markush cores in combinations with R-group fragments, at the fingertips of drug discovery chemists for ideal generation, data mining, lead hopping, as well as analysis related to IP positions. This talk will cover a recent work at Merck to construct a virtual chemical space powered by ChemAxon’s search engine and a few poetical applications planned.

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ChemAxon has been developing chemical data management tools, toolkits and applications for 16 years, primarily to the life science industry. Over this time, changes in the industry and technology have led change in our technology and how we work with clients. This talk outlines the ChemAxon functionality, breaking the topic down into processes scientists care about (creation, storage, analysis & reporting), highlights developments and our response to the opportunities in this changing environment.

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Markush structures are widely used in combinatorial libraries and chemical patents. However, the flexibility and complexity of Markush structures make them difficult to create, index, visualize, search, and enumerate. Recent improvement of ChemAxon’s applications makes Markush structure handling easier and more efficient. This presentation will give an overview abouth ChemAxon’s advanced Markush technology, including visualization, representation, search and enumeration. Our newly developed Markush Editor, Markush Composer and Markush Overlap Analysis tools will be introduced as well.

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As scientists we need to deal with inordinate amounts of data every day: we generate, retrieve and manipulate new data as part of our job. Simple excel worksheets are not the solution in the modern era of drug discovery, development and beyond. In this session learn how you can use and integrate ChemAxon’s tools to solve your day-by-day tasks more quickly and efficiently. Whether you prefer a desktop, web-based or touch screen application, we have a solution. Learn how to manipulate your data using Instant JChem (on your desktop or via Web layer) or draw sophisticated queries using Marvin or our new addition Marvin for Java Script (Marvin JS) to reduce the search times, visualize your data in 3D using Marvin Space, export and explore chemistry with the Ubiquitous Excel using the JChem for Excel plugin and share ideas and data with you colleagues and/or collaborators using Crais Board. Integrate our tools in Pipeline Pilot and Knime protocols and generate new data to expedite your processes. Analyze your data using Spotfire through Instant JChem. Also learn how our newest addition, Plexus, will help you do you tasks on desktop using web technology.

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The recent increase in utilization of complex macromolecules such as Antibody-Drug Conjugates (ADCs) as therapeutic agents has revealed a substantial gap in the biopharmaceutical industry’s portfolio of informatics tools and methods, most of which were designed to work primarily with either small molecules or unmodified and unconjugated amino acid and nucleotide sequences. The Hierarchical Editing Language for Macromolecules (HELM), along with a software toolkit that leverages that language was developed by Pfizer researchers to address this gap (see J. Chem. Inf. Model 2012, 52, 2796-2806). HELM and related technologies such as SCSR (Self-Contained Sequence Representation, see: JChem Inf Model. 2011 51, 2186-208.), enable the representation of unnatural, conjugated or otherwise modified building blocks in biopolymers such as oligonucleotides, peptides, proteins and ADCs. HELM is being released into the Open Source and the Pistoia Alliance has initiated a project that has the goals of (1) facilitating this release, (2) adopting HELM as an industry standard for the manipulation and exchange of complex biomolecule data, and (3) setting up the organizational infrastructure to govern the future development of the standard. Given the recent FDA approval of the Antibody Drug Conjugate Kadcyla (Ado-Trastuzumab Emtansine) for Her2-Positive Metastatic Breast Cancer, one can reasonably assume that standards such as HELM and associated software tools will play an increasingly prominent role as part of the modern drug discovery informatics arsenal.

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Foundation models are machine learning models which are easily capable of performing variable tasks on large and huge datasets. FMs have managed to get a lot of attention due to this feature of handling large datasets. It can do text generation, video editing to protein folding and robotics. In case we believe that FMs can help the hospitals and patients in any way, we need to perform some important evaluations, tests to test these assumptions. In this review, we take a walk through Fms and their evaluation regimes assumed clinical value. To clarify on this topic, we reviewed no less than 80 clinical FMs built from the EMR data. We added all the models trained on structured and unstructured data. We are referring to this combination of structured and unstructured EMR data or clinical data.

Reassessing the Bedrock of Clinical Function Models: An Examination of Large ...

Reassessing the Bedrock of Clinical Function Models: An Examination of Large ...

Reassessing the Bedrock of Clinical Function Models: An Examination of Large ...

harshavardhanraghave

Investing in AI transformation today The modern business advantage: Uncovering deep insights with AI Organizations around the world have come to recognize AI as the transformative technology that enables them to gain real business advantage. AI’s ability to organize vast quantities of data allows those who implement it to uncover deep business insights, augment human expertise, drive operational efficiency, transform their products, and better serve their customers

Microsoft AI Transformation Partner Playbook.pdf

Microsoft AI Transformation Partner Playbook.pdf

Microsoft AI Transformation Partner Playbook.pdf

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In today's dynamic e-commerce landscape, the payment gateway emerges as a linchpin, ensuring smooth and secure transactions between buyers and sellers. In this discourse, we delve into the meticulous process of devising test cases tailored for scrutinizing payment gateways. Crafting precise test cases for payment gateways is a quintessential responsibility for testers operating within the service industry. This article meticulously explores pivotal scenarios integral to how to test payment gateways, coupled with essential guidelines for drafting effective test cases.

Payment Gateway Testing Simplified_ A Step-by-Step Guide for Beginners.pdf

Payment Gateway Testing Simplified_ A Step-by-Step Guide for Beginners.pdf

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Test automation is a cornerstone of software development and quality assurance in today's rapidly evolving digital landscape. Its significance cannot be overstated. Businesses can enhance efficiency, productivity, and accelerate software delivery to market through automation, streamlining testing processes effectively. This comprehensive guide addresses the best practices for test automation in 2024. It offers a detailed checklist to empower you to optimize your automation efforts and maintain a competitive edge.

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The Ultimate Test Automation Guide_ Best Practices and Tips.pdf

The Ultimate Test Automation Guide_ Best Practices and Tips.pdf

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Conference: Engage2024 in Antwerp Type: Workshop Speakers: Florian Vogler, Henning Kunz, Christoph Adler Title: Navigating the Future with The Hitchhiker's Guide to Notes and Domino 14 Abstract: Embark on an exhilarating journey with industry trailblazers Florian Vogler, Henning Kunz, and Christoph Adler in this not-to-be-missed workshop at the forefront of the tech universe. Get ready for a thrilling kick-off as we navigate the current state of the HCL universe, setting the stage for an exploration of the groundbreaking Notes and Domino 14. Discover the latest enhancements and revolutionary features that will redefine your experience. In this interactive session, unlock a treasure trove of tips and tricks to elevate your utilization of version 14, both with and without the game-changing panagenda MarvelClient. Brace yourself for also diving into Nomad, Nomad Web, and VoltMX, expanding your horizons in the expansive HCL landscape. Be a part of this exclusive opportunity to stay ahead in the ever-evolving world of HCL technologies. Your journey to mastering Notes and Domino 14 begins here. And remember, in the spirit of intergalactic exploration, don't forget to bring your towel!

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W01_panagenda_Navigating-the-Future-with-The-Hitchhikers-Guide-to-Notes-and-D...

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ADR, or Architecture Decision Record, is a valuable tool in software development for several reasons. It provides a centralized location for documenting and tracking architectural decisions, aiding both current and future team members. ADRs enhance communication among team members by documenting the rationale behind architectural decisions, especially beneficial during onboarding of new team members or when revisiting decisions. They serve as a knowledge base, enabling teams to learn from past decisions and refine their decision-making process. Additionally, ADRs contribute to transparency by helping stakeholders understand the reasons behind specific architectural choices. As with any other tool or process, introducing them into an organization can face several obstacles, and overcoming these challenges is crucial for successful implementation. In this talk I go through some common problems and our way of solving them.

Architecture decision records - How not to get lost in the past

Architecture decision records - How not to get lost in the past

Architecture decision records - How not to get lost in the past

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Data spaces in distributed environments should be allowed to evolve in agile ways providing data space owners with large flexibility about which data they store. Agility and heterogeneity, however, jeopardize data exchanges because representations may build on varying ontologies and data consumers may not rely on the semantic correctness of their queries in the context of semantically heterogeneous, evolving data spaces. Graph data spaces are one example of a powerful model for representing and querying data whose semantics may change over time. To assert and enforce conditions on individual graph data spaces, shape languages (e.g SHACL) have been developed. We investigate the question of how querying and programming can be guarded by reasoning over SHACL constraints in a distributed setting and we sketch a picture of how a future landscape based on semantically heterogeneous data spaces might look like.

Shapes for Sharing between Graph Data Spaces - and Epistemic Querying of RDF-...

Shapes for Sharing between Graph Data Spaces - and Epistemic Querying of RDF-...

Shapes for Sharing between Graph Data Spaces - and Epistemic Querying of RDF-...

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Reassessing the Bedrock of Clinical Function Models: An Examination of Large ...

Reassessing the Bedrock of Clinical Function Models: An Examination of Large ...

Reassessing the Bedrock of Clinical Function Models: An Examination of Large ...

Microsoft AI Transformation Partner Playbook.pdf

Microsoft AI Transformation Partner Playbook.pdf

Microsoft AI Transformation Partner Playbook.pdf

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The Ultimate Test Automation Guide_ Best Practices and Tips.pdf

The Ultimate Test Automation Guide_ Best Practices and Tips.pdf

The Ultimate Test Automation Guide_ Best Practices and Tips.pdf

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EUGM 2014 - Eufrozina Hoffmann (ChemAxon): Smart Drawing with Marvin JS

1. Smart Drawing with Marvin JS Efi Hoffmann

2. Marvin: Drawing&Displaying Marvin for JavaScriptMarvin AppletMarvin Beans Web Desktop & Server Java JavaScript

3. Marvin JS • lightweight web component -> Architecture JavaScript, Html5, CSS3 • only a browser is needed to run • easy to integrate • fast startup, fast download • ready for tablets Client ServerMRV Web ServiceMarvin JS

4. New techniques Features Challenge Opportunity

7. 7 Electron flow arrows

8. 8 GUI Presets

9. Coming soon... (6.4) • Custom templates (server side) • Basic 3D & display options 9

10. Future plans More query feature: -reaction query -query atomic properties -link node ... 10

11. Thank you for your attention!