The document discusses scaling metagenome assembly to very large datasets. It proposes two approaches: 1) Partitioning the de Bruijn graph to divide the data into smaller, independent components that can be assembled in parallel. However, partitioning faces the same challenges of scaling to large datasets as other assemblers. 2) Digital normalization, which "squashes" redundant high coverage reads in a single pass to reduce the total data while preserving sequence content and gene coverage. Initial assemblies of field samples demonstrate the approaches can assemble petabase-scale datasets on a single compute node. Future work involves optimizing partitions, scaling implementations, and integrating other data types.
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Proteins. 2013 Nov;81(11):1885-99. doi: 10.1002/prot.24330. Epub 2013 Aug 16.
DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches.
Liu R, Hu J.
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Proteins. 2013 Nov;81(11):1885-99. doi: 10.1002/prot.24330. Epub 2013 Aug 16.
DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches.
Liu R, Hu J.
Circles of San Antonio Community Coalition is a program of the San Antonio Council on Alcohol and Drug Abuse SACADA). This presentation was used during a new SACADA board member orientation.
This seminar was given to clients and friends of the Columbus, Ohio, law firm of Kegler, Brown, Hill & Ritter on March 11, 2010. Topics covered include USERRA, hiring and firing, employment law updates, workplace investigations, employee benefits, COBRA, HIPAA, ERISA, harassment, discrimination and more.
Ejemplo de integración de un analizador léxico (lexer) y un analizador sintáctico (parser) implementados en JLex y CUP. Fuente: http://www.cis.uab.edu/courses/cs602/
Big Data for International DevelopmentAlex Rascanu
Alex Rascanu delivered the "Big Data for International Development" presentation at the International Development Conference that took place on February 7, 2015 at University of Toronto Scarborough.
Circles of San Antonio Community Coalition is a program of the San Antonio Council on Alcohol and Drug Abuse SACADA). This presentation was used during a new SACADA board member orientation.
This seminar was given to clients and friends of the Columbus, Ohio, law firm of Kegler, Brown, Hill & Ritter on March 11, 2010. Topics covered include USERRA, hiring and firing, employment law updates, workplace investigations, employee benefits, COBRA, HIPAA, ERISA, harassment, discrimination and more.
Ejemplo de integración de un analizador léxico (lexer) y un analizador sintáctico (parser) implementados en JLex y CUP. Fuente: http://www.cis.uab.edu/courses/cs602/
Big Data for International DevelopmentAlex Rascanu
Alex Rascanu delivered the "Big Data for International Development" presentation at the International Development Conference that took place on February 7, 2015 at University of Toronto Scarborough.
Tensors Are All You Need: Faster Inference with HummingbirdDatabricks
The ever-increasing interest around deep learning and neural networks has led to a vast increase in processing frameworks like TensorFlow and PyTorch. These libraries are built around the idea of a computational graph that models the dataflow of individual units. Because tensors are their basic computational unit, these frameworks can run efficiently on hardware accelerators (e.g. GPUs).Traditional machine learning (ML) such as linear regressions and decision trees in scikit-learn cannot currently be run on GPUs, missing out on the potential accelerations that deep learning and neural networks enjoy.
In this talk, we’ll show how you can use Hummingbird to achieve 1000x speedup in inferencing on GPUs by converting your traditional ML models to tensor-based models (PyTorch andTVM). https://github.com/microsoft/hummingbird
This talk is for intermediate audiences that use traditional machine learning and want to speedup the time it takes to perform inference with these models. After watching the talk, the audience should be able to use ~5 lines of code to convert their traditional models to tensor-based models to be able to try them out on GPUs.
Outline:
Introduction of what ML inference is (and why it’s different than training)
Motivation: Tensor-based DNN frameworks allow inference on GPU, but “traditional” ML frameworks do not
Why “traditional” ML methods are important
Introduction of what Hummingbirddoes and main benefits
Deep dive on how traditional ML models are built
Brief intro onhow Hummingbird converter works
Example of how Hummingbird can convert a tree model into a tensor-based model
Other models
Demo
Status
Q&A
The Next-Generation sequencing data-deluge requires storage and compute services to be provisioned at an ever-increasing rate. Can Cloud (and last decade's buzzword, Grid), help us?
Talk given at the NHGRI Cloud computing workshop, 2010.
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.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
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.
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.
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
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.
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Mission to Decommission: Importance of Decommissioning Products to Increase E...
Scaling metagenome assembly
1. Scaling metagenome assembly –to infinity and beeeeeeeeeeyond! C. Titus Brown et al. Computer Science / Microbiology Depts Michigan State University In collaboration with Great Prairie Grand Challenge (Tiedje, Jansson, Tringe)
3. Sampling strategy per site 1 M 1 cM 10 M 1 cM Reference soil 1 M Soil cores: 1 inch diameter, 4 inches deep Total: 8 Reference metagenomes + 64 spatially separated cores (pyrotag sequencing) 10 M
5. Our perspective Great Prairie project: there is no end to the data! Immense biological depth: estimate ~1-2 TB (10**12) of raw sequence needed to assemble top ~20-40% of microbes. Improvements in sequencing tech Existing methods for scaling assembly simply will not suffice: this is a losing battle. Abundance filtering XXX Better data structures XXX Parallelization is not going to be sufficient; neither are advances in data structures. I think: bad scaling is holding back assembly progress.
6. Our perspective, #2 Deep sampling is needed for these samples Illumina is it, for now. The last thing in the world we want to do is write yet another assembler…pre-assembly filtering, instead. All of our techniques can be used together with any assembler. We’ve mostly stuck with Velvet, for reasons of historical contingency.
7. Two enabling technologies Very efficient k-mer counting Bloom counting hash/MinCount Sketch data structure; constant memory Scales ~10x over traditional data structures k-independent. Probabilistic properties well suited to next-gen data sets. Very efficient de Bruijn graph representation We traverse k-mers stored in constant-memory Bloom filters. Compressible probabilistic data structure; very accurate. Scales ~20x over traditional data structures. K-independent. …cannot directly be used for assembly because of FP.
8. Approach 1: Partitioning Use compressible graph representation to explore natural structure of data: many disconnected components.
9. Partitioning for scaling Can be done in ~10x less memory than assembly. Partition at low k and assemble exactly at any higher k (DBG). Partitions can then be assembled independently Multiple processors -> scaling Multiple k, coverage -> improved assembly Multiple assembly packages (tailored to high variation, etc.) Can eliminate small partitions/contigs in the partitioning phase. In theory, an exact approach to divide and conquer/data reduction.
11. Partitioning challenges Technical challenge: existence of “knots” in the graph that artificially connect everything. Unfortunately, partitioning is not the solution. Runs afoul of same k-mer/error scaling problem that all k-mer assemblers have… 20x scaling isn’t nearly enough, anyway
13. Partitioning challenges Unfortunately, partitioning is not the solution. Runs afoul of same k-mer/error scaling problem that all k-mer assemblers have… 20x scaling isn’t nearly enough, anyway
14. Approach 2: Digital normalization “Squash” high coverage reads Eliminate reads we’ve seen before (e.g. “> 5 times”) Digital version of experimental “mRNA normalization”. Nice algorithm! Single-pass Constant memory Trivial to implement Easy to parallelize / scale (memory AND throughput) “Perfect” solution? (Works fine for MDA, mRNAseq…)
15. Digital normalization Two benefits: Decrease amount of data (real, but redundant sequence) Eliminate errors associated that redundant sequence. Single-pass algorithm (c.f. streaming sketch algorithms)
16. Digital normalization validation? Two independent methods for comparing assemblies… by both of them, we get very similar results for raw and treated.
17. Comparing assemblies quantitatively Build a “vector basis” for assemblies out of orthogonal M-base windows of DNA. This allows us to disassemble assemblies into vectors, compare them, and even “subtract” them from one another.
18. Running HMMs over de Bruijn graphs(=> cross validation) hmmgs: Assemble based on good-scoring HMM paths through the graph. Independent of other assemblers; very sensitive, specific. 95% of hmmgsrplB domains are present in our partitioned assemblies. CTC ACT TTC GTA GAC ATA ACC CTA Jordan Fish, Qiong Wang, and Jim Cole (RDP) GTT
19. Digital normalization validation Two independent methods for comparing assemblies… by both of them, we get very similar results for raw and treated. Hmmgs results tell us that Velvet multi-k assembly is also very sensitive. Our primary concern at this point is about long-range artifacts (chimeric assembly).
20. Techniques Developed suite of techniques that work for scaling, without loss of information (?) While we have no good way to assess chimeras and misassemblies, basic sequence content and gene content stay the same across treatments. And… what, are we just sitting here writing code? No! We have data to assemble!
21. Assembling Great Prairie data, v0.8 Iowa corn GAII, ~500m reads / 50 Gb => largest partition ~200k reads 84 Mb in 53,501 contigs > 1kb. Iowa prairie GAII, ~500m reads / 50 Gb => biggest ~100k read partition 102 MB in 70,895 contigs > 1kb. Both done on a single 8-core Amazon EC2 bigmem node, 68 GB of RAM, ~$100. (Yay, we can do it! Boo, we’re only using 2% of reads.) No systematic optimization of partitions yet; 2-4x improvement expected. Normalization of HiSeq is also yet to be done. Have applied to other metagenomes, note; longer story.
22. Future directions? khmer software reasonably stable & well-tested; needs documentation, software engineering love. github.com/ctb/khmer/ (see ‘refactor’ branch…) Massively scalable implementation (HPC & cloud). Scalable digital normalization (~10 TB / 1 day? ;) Iterative partitioning Integrating other types of sequencing data (454, PacBio, …)? Polymorphism rates / error rates seem to be quite a bit higher. Validation and standard data sets? Someone? Please?
29. Knots in the graph are caused by sequencing artifacts.
30. Identifying the source of knots Use a systematic traversal algorithm to identify highly-connected k-mers. Removal of these k-mers (trimming) breaks up the knots. Many, but not all, of these highly-connected k-mers are associated with high-abundance k-mers.
34. Our current model Contigs are extended or joined around artifacts, with an observation bias towards such extensions (because of length cutoff). Tendency is for a long contig to be extended by 1-2 reads, so artifacts trend towards location at end of contig. Adina Howe
35. Conclusions (artifacts) They connect lots of stuff (preferential attachment) They result from something in the sequencing (3’ bias in reads) Assemblers don’t like using them The major effect of removing them is to shorten many contigs by a read.
36. Digital normalization algorithm for read in dataset: if median_kmer_count(read) < CUTOFF: update_kmer_counts(read) save(read) else: # discard read
38. Per-partition assembly optimization Strategy: Vary k from 21 to 51, assemble with velvet. Choose k that maximizes sum(contigs > 1kb) Ran top partitions in Iowa corn (4.2m reads, 303 partitions) For k=33, 3.5 mb in 1876 contigs > 1kb, max 15.7 kb For best k for each partition(varied between 31 and 47), 5.7 mb in 2511 contigs > 1kb, max 51.7 kb
39. Comparing assemblies quantitatively Build a “vector basis” for assemblies out of orthogonal M-base windows of DNA. This allows us to disassemble assemblies into vectors, compare them, and even “subtract” them from one another.
Thank organizers; point to talk online. Mention Susannah/first asst prof problem.
1) Very high diversity ~30 billion k-mers. 2) No k-mer overlap between Iowa corn and prairie; co-assembly futile.
Indicate “surprising/awesome” components.
Connectivity source organism abundance
Comparing assemblies is hard, and we’ve had to build tools to build tools to let us compare assemblies. However, the results are good. Multi-k assemblies are essential, note.
Completely different style of assembler; useful for cross validation.
Note that all of this was done on Amazon in 68gb
Move towards loosely coupled environment for lossless approaches to scaling assembly? Weak classifiers & boosting theory can also be applied (trivially). Note, at some point you should just sequence single cells or something.