Article in Drug Discovery World: Data-driven transformation in drug discovery

By on July 17, 2018 in Blog, News

 

The Summer edition of Drug Discovery World contains an article by Dr Satnam Surae, Aigenpulse Chief Product Officer, on Data-Driven Transformation in drug discovery.

It reviews the current approach to data management and its application within the drug development and research setting, highlighting major critical challenges and emerging solutions for organisations that need to harness big data and machine learning. What will the future of R&D look like in 10 years?

Read the article to learn about:

  1. Meeting the challenge of compliance & complexity.
  2. Embracing a data-based revolution
  3. Being truly data-driven
  4. Machine learning driving informed decision making
  5. Digital transformation in data management
  6. Future perspectives

 

 

 

Come and meet Aigenpulse at ON Helix

By on June 27, 2018 in Blog, News


Tobias will be chairing the ON Helix “AI in Drug Discovery” panel session at 2pm on July 11th in the King’s Hedges room at The Cambridge Building, Babraham Research Campus.  It should be a really interesting session with Peyman Gifani from AI VIVO and Mark Rackham from BenevolentAI.  A good opportunity to find out more about how Artificial Intelligence is being applied in the Life Sciences sector.

Impressions of the March Bioinformatics London Meetup

By on April 5, 2018 in Blog

Impressions of the March Bioinformatics Meetup at Hays Recruitment in London.
The meeting was chaired by Stephen Newhouse and hosted by Ben van Zwanenberg at the rather smart Hays Life Sciences Recruitment Offices in Cheapside.
As we mentioned previously, we enjoy attending smaller meetups like this one as they are a great way of keeping up to date.

In this meeting Ian Harrow explained the Pistoia Alliance, Ontologies Mapping project
Ian started his talk by putting the Pistoia Alliance into context; it is a global not-for profit alliance of Pharma and Healthcare organisations who recognised that collaborative precompetitive research could bring value to the industry and thus to healthcare as a whole. There are 4 main themes within the Alliance:

  • Building new standards
  • Sharing best practice
  • Evaluation of tools & services
  • Projects

But maybe one of the biggest benefits is “Cutting through corporate mud”!
There are 68 paying members, which is pretty impressive
We learnt about the application of Ontologies Mapping. Basically, Ontologies describe hierarchical relationships and are critical for effective scientific search and data integration. In a biological/biomedical setting the hierarchy comprises:

  1. Class
  2. Class Hierarchy
  3. Identifier

There are already a broad range of public ontologies. When domains overlap it is quickly found that multiple ontologies need to be utilised. And when there are multiple ontologies e.g. disease & phenotype it becomes important to map them. As Ian says “you can’t munge ontologies together or you end up with a Frankenstein approach.”

A better approach is to map the source ontologies. There will always be challenges with maintaining the ontologies, however, maintaining the map is much more tractable and simple. This is a much easier, cheaper & better engineering solution.
And there is a lot to do because much of science is in unstructured ‘stuff’!

The Pistoia Ontology Mapping Project
Ontologies are the smart glue of linked data to semantically enable knowledge management. However, an ontology is “like having a baby – once a new one arrives it takes maintenance and costs money”!
The Pistoia Project provides:

  1. Guidelines for best practice
    A 15-point checklist
    NB it is important to be aware of the health of the ontologies that are being used
  2. Evaluation of tools
    Several commercial & academic tools were evaluated
  3. A Prototype service

Pistoia is working with EMBL-EBI* to develop a new algorithm for an ontologies mapping service. Source ontologies being mapped change rapidly so mappings have to be maintained as a service. Ontologies and their mappings are specific to particular domains in the Life sciences. These are often much more complex than other sciences such as astronomy, chemistry or physics due to the heterogeneity of the data.

I really enjoyed the meetup – bioinformatics is moving at such a rapid pace, that such events are a really good way of keeping up-to-date. At Aigenpulse, we’re also developing next generation solutions for structuring and integrating biological data and we’ve found that mapping biological entities to ontologies is a critical task in many of our clients’ pipelines and creates a large overhead. The talk reaffirmed this issue and it was great seeing a collaborative effort to develop solutions to alleviate this challenge – and is something in which we, at Aigenpulse, will be getting a lot more involved. I learnt a lot and met some really interesting people, so I’ll be signing up for the next one in May. https://www.meetup.com/Bioinformatics-London/events/ksqwtmyxhbpc/
*The European Molecular Biology Laboratory -European Bioinformatics Institute

Impressions of the March DevOps Oxford Meetup

By on March 29, 2018 in Blog

I attended the DevOps Oxford Meetup on Tuesday evening at the Oxford Centre for Innovation. This was my first time attending an event held by the group and I’ll definitely be attending again!

This particular meetup was a collection of lightning talks – 6 x 10-minute presentations with Q&A – about all things DevOps. DevOps is a portmanteau of Development Operations and, from my understanding, is better described as a culture rather than a defined discipline – because it brings together so many elements from the spectrum of software development, system administration and technology operations – with the aim of delivering applications or products at a high pace whilst maintaining reliability, security and scale.

We were greeted with nibbles and beers and had a few minutes to mingle with other attendees. The first batch of talks were more technically focused explaining such issues as simplifying Dockerfiles; the advantages of using Project Atomic tools and Kubernetes/OpenShift over the standard Docker packages; migrating to and implementing Kubernetes infrastructure on Azure. These talks and the following Q&A were very informative and made me realise how far these containerisation and orchestration technologies have come in a relatively short space of time.

The second batch of talks began with a view of the DevOps marketplace which highlighted the need of employers to really think about what they are trying to achieve in hiring a DevOps. Then we were treated to a talk about the novel uses of IoT (internet of things) for optimising building heat usage. And finally, a very high-level overview as to why DevOps should make friends with biologists – where the speaker outlined the massive transformation happening within the science and the need for technical expertise to help unravel the complexity of biology.

The Meetup was a great event, with many very well-versed attendees asking some very complex questions. I took a lot away from the event and will definitely be attending (and maybe even presenting) at a future event.

Here at Aigenpulse, our engineering teams are living the DevOps culture with our focus on rapid delivery & fast iteration whilst maintaining security and stability. I can see now that these DevOps Meetups are great for us because we’re passionate about staying up-to-date and engaging with like-minded people at the forefront of technology!

Data Technology as a Catalyst for Growth in the Life Sciences

By on March 28, 2018 in Publications, White Paper

What is Big Data? How can 1) the Life Sciences Sector Capitalise on Data Technologies? 2) you Establish the Right Environment? 3) Enable a Culture of Success? What are the Keys for Success? Our White Paper has the answers.

 

Download “Data Technology as a Catalyst for Growth” Data_Catalyst_Growth_aigenpulse-whitepaper-final.pdf – Downloaded 132 times – 2 MB

Aigenpulse at BioTrinity 2018

By on March 23, 2018 in Blog

Aigenpulse is exhibiting at BioTrinity on 23rd-25th April in London.

We’re on stand 23, so do visit us there; we’d love to see you!

Our CEO Tobias Kloepper will also be chairing a panel and speaking at the BioLaunchPad at 11:10am on Tuesday 24th April in Plenary Hall 2, so even more opportunity to see what we do!