We're launching our very first Webinar! by Gabriella Jonasson

On April 26th at 4 pm CET, we're broadcasting our very first live Webinar - Biomolecular structures: How to maximize the value of what you already have. Save your seat by registering today!

In this introductory webinar, our speaker Dr. Peter Schmidtke, Scientific Project Manager at Discngine, will list current pitfalls in structure-based drug discovery and introduce how we are intending to address these in our cloud-based solution 3decision®.

We will also show use cases highlighting the importance of good data management, persistence as well as proper handling of metadata in the scope of structure-based drug design projects.

Last, we will show an outline of the next decades of structure generation, emphasizing why proper structure management will become increasingly important.

This is the first Webinar in a series that will cover the benefits and potential of good structural knowledge management. Space will be limited, click to register!

Optimized Storage and Querying for Matched Molecular Pairs: The MMP Database by Raphaël Berthier

Matched Molecular Pairs Analysis (MMPA) is a widely used method to analyse molecular structure, property and activity relationships. It allows to extract frequently observed transformations, and associate property or activity changes to these structural modifications. One of the main advantages of MMPA lies in its intuitiveness and the easy interpretation of results, therefore making it one of the most important tools in the medicinal chemist toolbox.

In this blogpost we will present our latest developments to handle more efficiently large MMP datasets and databases, how to keep them up to date and how to develop responsive applications on top of that. 

What are Matched Molecular Pairs?

A Matched Molecular Pair, or MMP, can be defined as a pair of molecules sharing a common structural part, and only differing through a well-defined structural modification. Thus, an MMP defines a transformation between two molecules. On the right is depictured an MMP, with the common structural part (called Core, coloured in grey), and the two variable parts (called Fragments, coloured in red) defining the transformation in the MMP. Molecules within a given MMP can therefore be converted to one another by chemically modifying a specific fragment into another.

How are MMPs used?

MMPA relies on finding all MMPs within a given dataset, computing the corresponding change in property or activity between the two molecules of each pair, and associate this difference to a chemical transformation. A given transformation, if observed a sufficient number of times, can give an overview of what could happen if it is applied to other molecules: the robustness of predictions that can be made with MMPA is therefore directly related to the amount of data available. Thus, MMPA is increasingly useful with increasing dataset sizes.

Since we’ve been working with MMPs for quite a while now, you can check out a more complete overview of what are MMPs and how they are used by computational and medicinal chemist in this previous Chemistry Collection release article, presenting Matched Molecular Pair Analysis Components for Target Activity Prediction on Small Datasets The “Context” of an MMP will not be detailed here but is thoroughly explained in the linked article.

MMPs issues in pharmaceutical R&D

When generating MMPs on large corporate databases large amounts of data are inherently generated. This data must be properly organized for drug discovery scientists to be able to use it in an efficient manner.  From what we’ve heard and seen, the methods used to store MMPs have one or more limitations: either the high response time for a given query on MMPs (e.g. What is the general effect of this transformation regarding this chemical property?), the time to update the MMPs with new molecules (which usually requires computing all MMPs for each update), or the ability to store several representations of the context for a given MMP. Methods used today result in poor performance for MMPA-based applications. As a result only part of the molecules that should be contained in such applications are contained. Furthermore they are not updated on a fast and regular pace. Last, MMPs are usually calculated “on-the-fly” on smaller datasets: a more convenient solution but far from being time-efficient and having robust predictions with high statistical significance.

 The Matched Molecular Pairs database

For the past months, we have been developing and testing a new Matched Molecular Pair Database model, and the Pipeline Pilot Toolbox that goes along with it. The Oracle database model delivered with the Discngine Chemistry Collection enables MMP storage for millions of molecules, frequent and fast updates, while retaining time-efficient MMP-related queries. Additionally, several specific chemical context types for each MMP can be added independently, and at any time. This database can then easily be integrated in existing application (e.g. Pipeline Pilot, TIBCO Spotfire, Web Service integration, Database integration…)

Retrieving all MMPs for a given molecule, a fragment, or a transformation with or without context specification is now only a matter of seconds, even for datasets of millions of molecules. Updating your MMPs with new structures is now done in a few seconds. It goes without saying that this includes both multi-cut MMPs and MMPs with hydrogen fragments.

Moreover, now you can have a much finer control on the identification of MMPs (i.e. which MMPs are to be formed and which are not, the molecular bonds to ignore, the size of fragments and cores…), and can use specific MMP identification rules (e.g. RECAP-MMPs) . Specific core chemical contexts for each MMP can also be generated independently: in addition to the classic core chemical context representation provided by Pipeline Pilot, this Discngine Chemistry Collection release also includes the availability to generate and store multiple context representations (e.g. Pharmacophore Graph context representation), including your own definition of context, for each MMP.

A few benchmarks values

From the benchmarks we’ve run on a MMP database of 1 million molecules (with more than 90 Million MMPs generated): the average response time for querying all MMPs for a single molecule was 0.5 seconds, the average response time for querying the database for a given transformation is 0.03 seconds, and the time for updating the MMP Database with 2,000 new molecules never took more than 1 minute.

Key Benefits

This Discngine Chemistry Collection release with its new optimized storage and querying for MMPs feature can allow you to boost the performances on your MMPA-based tools with a finer control on MMP identification, to gain statistical significance on your MMPA property predictions, and to perform MMPA on both your in-house and your vendors’ catalogues structures. Moreover, it allows to generate new context representations of your own, and to perform MMPA on the non-registered medicinal chemist’s ideas. 

The Matched Molecular Pair database can also be used to generate Matched Molecular Series (i.e., a series of analogue compounds having a common substructure and different fragments, thus, all being MMPs with one another), and identify common scaffolds in a given series of analogue compounds. With the use of MMPs and MMSs, navigating through your SAR and making property/activity predictions with a wide range of MMPA methodologies becomes now much easier, and with improved statistical robustness.

Integration examples

Here a few integration examples that we’ve done with our MMP database, Pipeline Pilot, Oracle and TIBCO Spotfire.

Job position - Experienced Front-End Web developer by Gabriella Jonasson

Discngine is one of the leading independent life sciences research software integrators and application developers.

From its inception in 2004 our mantra has been to deliver scientific solutions in order to transform the R&D centers research systems into innovative and intelligent discovery platforms.

Discngine acts as a partner in each phase of the client project, from the design to the delivery of a software solution that supports any research process. Discngine is a dynamic company capitalizing on key skills, rooted in the well-established quality of its consultants.

In order to enforce our R&D team we are hiring a highly-motivated and experienced front-end web developer who will work in our main offices in Paris (France).

What you will be assigned to

You will join the SCRUM team developing 3decision – a next generation structural knowledge management solution. You will contribute with your experience and vision in front-end web development.

You will play a central role in the management and development of the project:

  • Conception and technical & functional front-end development, in close collaboration with the project team
  • Technical implementation in Angular JS (and preparation of a future migration) 
  • Integration and non-regression testing
  • Design development of the application user interface
  • Corrective and evolutionary maintenance of applications 
  • Technology watch (language, technical solutions...)

The profile we are looking for

You have a Master’s Degree, an Engineering Degree or an equivalent degree in Informatics, and have acquired significative development experience. You are passionate about web application development, especially in the scientific area. You develop modern and beautiful web interfaces that grant a good user experience.

Required web development qualifications (Expert Level):

  • HTML5, CSS3
  • Javascript
  • Web services REST
  • Angular JS
  • Node.js
  • Unit and functional testing framework

Other Qualifications:

  • Agile development environment 
  • Policy standards for development, tests and validation 

You also have good communication skills and can expose and understand complex technical problems with ease. You can efficiently discuss technical aspects in English. You like team work and you’re not afraid of complex environments. You are autonomous and curious, you like to take initiatives.

Send us your resume!

The position is based in Paris, 79 avenue Ledru-Rollin. Your salary will depend on your profile and experience.

You can contact us at jobs _ at _ discngine.com

Job Position - Junior Web Application Developer by Gabriella Jonasson

Discngine is one of the leading independent companies in the life sciences software industry, integrating and developing applications.  

Since our inception in 2004, we are dedicated to enable R&D scientists to discover active molecules faster. From drafting a blueprint to implementing solutions, we can partner and assist our customers in each phase of their projects. 

We are a dynamic company relying on the recognized key skills of our experienced collaborators. We also rely on an innovative management approach. Working at Discngine implies being involved in projects which aim to deliver high quality products and services. It also means you will work in an atmosphere based on trust, commitment, transparency, goodwill and simplicity. 

Our Customer Services team is seeking a highly-motivated junior Web Application developer who will work at our main offices in Paris (France)

Missions

You will use Agile frameworks (SCRUM, Kanban) and will take care of: 

  • Business requirements analysis 
  • Customer interaction 
  • Application and features development 
  • Scientific software package integration 
  • Test writing and execution 
  • Corrective & evolutionary maintenance 
  • Documentation writing 

Profile

You have a Master’s Degree, an Engineering Degree or an equivalent degree in Informatics, and you are strongly interested in web application development, scientific research and pharmaceutical industry. 

You have a good understanding of and ideally have already used: 

  • Relational databases: Oracle Database, PL/SQL, SQL 
  • Web development: HTML, CSS, Javascript, REST web services 
  • Versioning tools: Git 

Knowledge in the Oracle Application Express framework or in BIOVIA Pipeline Pilot would be beneficial. 

You can efficiently discuss technical aspects in French. You put the customer at the center of your approach, you always try to give your best and are always looking for ways to improve, you are always willing to share your knowledge and you like to take initiatives.

If you recognize yourself in the description above, you'll probably love working at Discngine.

Send us your resume!

The position is based in Paris, 79 avenue Ledru-Rollin. Your salary will depend on your profile and experience.

You can contact us at jobs _ at _ discngine.com

Job Position - Web Developer by Alexandre Perret

Discngine is one of the leading independent companies in the life sciences software industry, integrating and developing applications. 

Since our inception in 2004, we are dedicated to enable R&D scientists to discover active molecules faster. From drafting a blueprint to implementing solutions, we can partner and assist our customers in each phase of their projects. 

We are a dynamic company relying on the recognized key skills of our experienced collaborators. We also rely on an innovative management approach. Working at Discngine implies being involved in projects which aim to deliver high quality products and services. It also means you will work in an atmosphere based on trust, commitment, transparency, goodwill and simplicity. 

Our R&D team is seeking a highly-motivated and experienced web developer with a solid background in statistics and/or data quality control who will work in our main offices in Paris (France).

Missions

You will be part of the SCRUM team in charge of developing the Discngine Qualification application. You will take care of: 

  • modeling, designing and analysing new tools 
  • developing new features (e.g. integration of statistical models) 
  • developing integration and non-regression tests
  • upgrading and supporting the application 
  • writing guides and tutorials in French and English

Profile

You have a Master’s Degree, an Engineering Degree or an equivalent degree in informatics, and you have acquired a significant experience in software development. You have a strong appeal for statistics.

You are highly motivated by application development in the research industry area.

You are proficient in:

  • Web development: HTML, Javascript (jQuery, d3.js, Oracle JET), CSS
  • Databases: Oracle Database, PL/SQL, SQL
  • Good Laboratory Practice (GLP) 
  • Agile frameworks (Kanban, SCRUM) 

You have a strong knowledge of:

  • Statistical methods in the field of quality  (e.g. Westgard rules) 
  • Version control tools (Git) 

Knowledge in the Oracle Application Express framework and in the IWA15 standards would be beneficial. 

You can efficiently discuss technical aspects in French. You put the customer at the center of your approach, you always try to give your best and are always looking for ways to improve, you are always willing to share your knowledge and you like to take initiatives.

If you recognize yourself in the description above, you'll probably love working at Discngine !

Send us your resume!

The position is based in Paris, 79 avenue Ledru-Rollin. Your salary will depend on your profile and experience.

You can contact us at jobs _ at _ discngine.com

Job Position - Statistician and Web Developer by Alexandre Perret

Discngine is one of the leading independent companies in the life sciences software industry, integrating and developing applications. 

Since our inception in 2004, we are dedicated to enable R&D scientists to discover active molecules faster. From drafting a blueprint to implementing solutions, we can partner and assist our customers in each phase of their projects. 

We are a dynamic company relying on the recognized key skills of our experienced collaborators. We also rely on an innovative management approach. Working at Discngine implies being involved in projects which aim to deliver high quality products and services. It also means you will work in an atmosphere based on trust, commitment, transparency, goodwill and simplicity. 

Our R&D team is seeking a highly-motivated and experienced statistician with a solid background in software development who will work in our main offices in Paris (France).

Missions

You will be part of the SCRUM team in charge of developing the Discngine Qualification application. You will take care of: 

  • modeling, designing and analysing new tools 
  • integrating statistical models
  • developing features, integration and non-regression tests
  • upgrading and supporting the application 
  • writing guides and tutorials in French and English

Profile

You have a Master’s Degree, an Engineering Degree or an equivalent degree in statistics/informatics, and you have acquired a significative experience in statistics and software development.

You are highly motivated by application development in the research industry area.

You are proficient in:

  • Statistical methods in the field of quality  (Westgard rules) 
  • Good Laboratory Practice (GLP) 
  • Agile frameworks (Kanban, SCRUM) 

You have a basic knowledge of:

  • Databases: Oracle Database, PL/SQL, SQL 
  • Web development: HTML, Javascript (jQuery, d3.js, Oracle JET), CSS
  • Version control tools (Git) 

Knowledge in the Oracle Application Express framework and in the IWA15 standards would be beneficial. 

You can efficiently discuss technical aspects in French. You put the customer at the center of your approach, you always try to give your best and are always looking for ways to improve, you are always willing to share your knowledge and you like to take initiatives.

If you recognize yourself in the description above, you'll probably love working at Discngine !

Send us your resume!

The position is based in Paris, 79 avenue Ledru-Rollin. Your salary will depend on your profile and experience.

You can contact us at jobs _ at _ discngine.com

The Newbie Backlog: How we welcome our new co-workers. by Sébastien Conilleau

Two years ago, at Discngine, we decided to rethink the way we welcome our new co-workers. We ended up with an onboarding process which we call the Newbie Backlog. It allows the new ones to acquire most of the basics they need to know, very quickly. Moreover, we observed that once the training period is over, the backlog remains a widely used information resource. We're convinced that our onboarding process is useful as it has been confirmed by the excellent feedback we got from the newbies themselves. However, very recently I was surprised to realize that this kind of process is rare, so I decided to share the full story with you. 

Once upon a time … 

"Remember the future" to improve your organization

2014-2015 was a major hiring period for us, we almost doubled the company size in less than a year. Before this period, the onboarding process was mostly technical with a few documents here and there, and it was mainly supported by one single person. We were only a few people in the company, so the very important non-technical information (who does what, where do I find this or that, how do I do this, etc.) was acquired by discussing with the rest of the people, and didn’t really need to be written somewhere before this hiring period. Although we almost didn't have any document, the beginners were very grateful and could successfully integrate the team without any problem. All this mostly thanks to the person who took so much time to train them. That process was very time consuming (imagine the amount of effort needed when doubling the company size in a few months!), so when we hired many people in 2014-2015, other colleagues took part to the training process. The unfortunate consequence, since there was no supporting documentation, was that the information passed was incomplete or different depending on the person welcoming the new colleague and, sometimes details were forgotten afterward. According to the feedback of our "2014 new colleagues", this process was not sufficient anymore

Fortunately, by the end of 2015, there was an inflection point: Discngine organized a 2-days offsite event on the Atlantic coast of France with the aim of deepening our knowledge and improve our practice of Scrum and other agile approaches in a relaxed and playful environment with a strong team-building component. The event was coached by Claude Aubry, our scrum Guru, and one of the last exercises was a game called “Remember the future”. We used it to quickly undercover things that were missing and would be very beneficial to work on to improve our organization. Amongst other things, we identified a strong need regarding the way we welcome, accompany and train our new colleagues. We even ended up with a quite comprehensive list of subjects people would like to be trained in or at least informed on. Of course, the fact that this subject popped up was influenced by the fact that most people in the company were quite new, but we had planned to hire more people, so the subject was hot! 

The birth of the newbie backlog 

newbie backlog for new co-workers

After the event, we quickly built a small team of 6 highly motivated people (Ariane, Claire, Géraldine, Nicolas, Vanessa & me). The team composition was pretty neat with both recently hired people and dinosaurs (I’m the dinosaur here), as well as people with experience from other companies and people without it. We listed up things we thought new employees needed to know early on. Thanks to the “Remember the future” workshop, it was a straightforward task. Everybody had some very good ideas of the kind of information that was needed. We ended up with a quite comprehensive list: 

  • technical training
  • technical environment (servers and this kind of stuff)
  • how to prepare the minimum viable computer
  • administrative information (how do you ask for vacations, where do you log your activity, …)
  • Discngine working habits (scrum framework and others agile approach, code versioning, …)
  • Business environment (our products, our clients, our partners and our competitors) 

We struggled more with the format it should have. We had the feeling that a file (typical Microsoft PowerPoint slide deck or Microsoft Word document) would not really hit the target. It’s boring and people can very quickly become passive, or even not read it. Moreover, we wanted the new co-workers to be introduced to the agile way we manage projects, and a file can only give you a theoretical explanation, not a practical exercise. Also, writing a good file with such an amount of data is a huge piece of work! I don’t even want to think about what it would take to keep it up to date at all time…. A colleague of ours, outside the team, had this idea that immediately stroke us as the solution: make it a project, use Trello for that too. It was a brilliant idea, I mean it. One of those that make you feel stupid for not finding it yourself (thank you again, Benjamin, I know you like making me feel stupid). Here we were! We had a precise idea of the content, and a good way to make it usable. 

A few days later, after hours of gathering and formatting the info (and after several beers), we had it!  The Newbie Backlog was born. 

Gurus 

Onboarding Guru

We had one last detail to set up before we could actually use the newbie backlog: How to keep one of the best things of the former way of doing: human relationship? We wanted to ensure that people would not get lost and that feedback regarding the onboarding process would flow back to our team. To address this, we needed to define a new role in the company: The Guru

At Discngine, a guru has nothing to do with spiritual leaders (we just thought it was a way cooler name than "mentor"). A Guru's only duty is to help the newbie walk through the newbie backlog, guide him or her towards autonomy and pass on the spirit of Discngine. When it works, it’s quite rewarding! Of course, all Gurus are volunteers, but it’s pretty easy to find people that want to be other one’s Guru ^^. 

Where we're now 

The newbie backlog has been in place for more than 2 years now, and about 20 people have used it during their training period. Of course, it has known maintenance, reformatting, updating, etc., to keep it alive and relevant. For instance, the technical training on our main framework used to be in a single card of the original Newbie Backlog. Recently we extracted it to a dedicated complementary backlog which guides the newbie in the development of a sample application with a list of features. With the help of the Guru, the newbie has to produce the sample application from scratch. We did this to enforce the project management aspect of the training, as well as to detect people’s (in)ability. 

Overall the feedback is excellent, so we’re quite proud of what we’ve achieved here. We think there’s a high sense of belonging among the people working at Discngine and it’s important to keep it this way. Engagement is one of our core values so it's crucial everyone feels that they belong here. From what we observed we believe the newbie backlog is an excellent way to reach this goal. It keeps the sense of belonging high because newbies can dive in very quickly and understand who we're, and how we work. This reason alone already makes it worthwhile. 

Let me finish off by saying that whether you're a newly graduated student or an already working developer/scientist, be sure that if you join us, you will have a pleasant onboarding journey!

We're starting a Slack community for our customers! Here's why. by Gabriella Jonasson

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At Discngine, we're always looking to build a relationship of trust and transparency with our customers. By using the SCRUM & Agile methodologies, we're able to give our clients more control and influence on the final product. We've now decided to take our customer relationship one step further by creating our own Slack community - the Discngine User Group. 

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Slack  is a really cool real-time team messaging app. The conversations can be held in both open and closed groups as well as in one-to-one discussions. We've been using it internally for over a year now. It quickly became extremely popular, to the point of reaching more than 300K messages in less than a year (with 35 users per week on average).  

We use Slack to discuss all kind of work-related (and unrelated) topics, either in general channels or in smaller working groups. We also use it to ask for advice on a technical problem and to communicate with coworkers working on a different location (and sometimes the ones right next to us, but that's another story). The arrival of Slack allowed us to significantly reduce the amount of mails and simplify the communication within the company.  

We now want to open this channel of communication to our customers and partners. Besides getting to know us even better, there are numerous benefits to this. 

The benefits of a Slack community 

It allows you to participate actively in a project  

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The real-time discussions allow you to get a quick answer to your question, directly from us here at Discngine. You can thus discuss technical questions with the developers or ask the product owner for more details on a specific feature.  

Slack also allows you to use one of the private channels to discuss directly with your dedicated Discngine project team on more sensitive information such as requirements or prices. 

It improves and simplifies your customer support 

If you choose to use Discngine User Group for your customer support, the current system of emails and support tickets will be replaced by one simple feed where all information can be viewed and searched in an easy manner.  

Slack’s real-time discussions make it very easy to collaborate, create clarity and refine requirements. By linking resources from other applications to the Slack discussion, all information can be found in one place.  

It creates a closer relationship

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Real-time conversations are usually more casual than the typical mail exchange. We hope that Discngine User Group will allow us to build a more personal relationship with you. We also hope that the direct access to us and the community conversations will create a friendly and amusing environment for your support.  

It allows you to stay informed on news and events 

Slack is also a very convenient way of staying up-to-date on our releases, product launches, webinars etc.  

You might also want to inform us about important business news on your side. This is what the private channels are for!  

It allows you to learn from others 

As mentioned above, Slack gathers public and private discussions on the same platform. This allows people across different companies to discuss specific topics directly with us but also with each other. This is a perfect way to share tips and tricks, benefit from other people's questions (and our responses of course) and share ideas.   

The Slack community is also a great welcoming for you who are new customers. It allows you to quickly get your questions and concerns addressed, and to understand what services are available for you.  

How to join the Discngine User Group

Sign up here!

To join us on Slack, sign up here and we'll send you an invite to join the Discngine User Group.  

Slack_signup.png

New to Slack?

Check out this guide on getting started for new members.

The code of conduct

In order to create a welcoming, inclusive community around Discngine, we have set up a code of conduct for the Discngine User Group: 

The Discngine User Group is dedicated to providing a safe, inclusive, welcoming, and harassment-free space and experience for all participants, regardless of gender identity and expression, sexual orientation, disability, physical appearance, socioeconomic status, body size, ethnicity, nationality, level of experience, age, religion (or lack thereof), or other identity markers. Our Code of Conduct exists because of that dedication, and we do not tolerate harassment in any form.

The rules  

To keep some order on the different channels, we also have set up 7 golden rules that we expect everyone to follow.

  1. English is the only language used in the public channels 

  2. Everyone can invite users as long as they belong to a customer or partner organization

  3. The customer email address is always hidden

  4. Your nick name should be first name followed by the company name (or acronym). E.g. peter dng, justin az, matt pfe

  5. Nobody is obligated to always answer right away

  6. Only admins & owners can use the mass notification functions (@channel, @here, and @everyone) 

  7. Admin & owners should use mass notification wisely 

Join our community! 

Talk to you soon, on Slack :)

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Images borrowed from Slack Help and Unsplash

Job position - Senior Oracle and Web Application Developer by Gabriella Jonasson

Discngine is one of the leading independent companies in the life sciences software industry, integrating and developing applications. 

Since our inception in 2004, we are dedicated to enable R&D scientists to discover active molecules faster. From drafting a blueprint to implementing solutions, we can partner and assist our customers in each phase of their projects. 

We are a dynamic company relying on the recognized key skills of our experienced collaborators. We also rely on an innovative management approach. Working at Discngine implies being involved in projects which aim to deliver high quality products and services. It also means you will work in an atmosphere based on trust, commitment, transparency, goodwill and simplicity. 

Our R&D team is seeking a highly-motivated and experienced full-stack developer (Oracle, Apex) who will work in our main offices in Paris (France).

Missions

You will use Agile frameworks (SCRUM, Kanban) and will take care of: 

  • Business requirements analysis 
  • Customer interaction 
  • Roadmaps & vision building 
  • Application architecture design 
  • Application and features development 
  • Scientific software package integration 
  • Test writing and execution 
  • Corrective & evolutionary maintenance 
  • Documentation writing 

Profile

You have a Master’s Degree, an Engineering Degree or an equivalent degree in Informatics, and you have acquired a significative experience in software development, ideally in an Agile context and in the pharmaceutical industry area. 

You are highly motivated by application development, especially in the Research area. You are proficient in: 

  • Relational databases: Oracle Database, PL/SQL, SQL 
  • Web development: HTML, CSS, Javascript, REST web services 
  • Versioning tools: Git 

Knowledge in the Oracle Application Express framework or in BIOVIA Pipeline Pilot would be beneficial. 

You can efficiently discuss technical aspects in French. You put the customer at the center of your approach, you always try to give your best and are always looking for ways to improve, you are always willing to share your knowledge and you like to take initiatives.

If you recognize yourself in the description above, you'll probably love working at Discngine.

Send us your resume!

The position is based in Paris, 79 avenue Ledru-Rollin. Your salary will depend on your profile and experience.

You can contact us at jobs _ at _ discngine.com

Discngine raises €1.1 million ($1.3M) in Series A funding round by Eric Le Roux

The company will push forward with its unique SaaS software offering for facilitating the discovery of innovative molecules

Paris, France, December 11, 2017 – Discngine, a software company specializing in applications for life sciences research, today announces a Series A financing round of €1.1 million ($1.3M), received from Extens Développement e-Santé. The funds raised will allow Discngine to move forward with its Software-as-a-Service (SaaS) solution offering for the life sciences industry, a model that is not, as yet, widely used in this sector. 
Discngine already offers software for data management, visualization and decision-making processes in the life sciences industry, with leading pharmaceutical and cosmetics firms among its clients. 
Besides speeding up the development and commercialization of its SaaS solution offering, the company will use the new funds to extend its international reach, as well as to hire ten new staff members by the end of 2018. The company will also establish a supervisory board, comprising of representatives from Extens and Discngine as well as two experts from the life sciences research sector: Gordon Waldron, from Sequoia Business Solutions and Simon Valentine, from Illumina. 
The Software-as-a-Service approach offers services to clients based on a subscription model. It is well established in several industries, with strong growth potential. In the life sciences sector however the model is not yet widespread. Discngine could be among the first companies to make it more accessible to clients, building on the company’s long-standing technical and scientific knowledge of 14 years. 
"Thanks to this investment, our team will be able to industrialize our high value-added projects and commercialize them via a SaaS (Software-as-a-Service) offer available to researchers all over the world," said Eric Le Roux, founder and CEO of Discngine. "Discngine now has the means to accelerate its international development."

"We are excited to invest in Discngine. The company has developed a state-of-the-art technology platform that increases the efficiency of drug discovery, helping to find ‘bankable’ molecules,” said Arnaud Houette, managing director of Extens. “The challenge is not only financial, but above all medical. This is a good example of our strategy: identifying French e-health startups that develop promising technologies, helping them accelerate their development - contributing to an improvement in our health system."

Discngine is already collaborating with Dassault Systèmes BIOVIA on the distribution of its first two SaaS solutions. It is also planning to launch new solutions dedicated to life sciences research in 2018. 
 

Investors: Extens (Cédric Berger, Arnaud Houette)
Financial Audit: ACA Nexia (Hervé Krissi, Olivier Duval)
IT Audit: Make it Work (Frédéric Thomas)
IP Audit: Astura (Matthieu Mélin, Robin Le Marois)
Legal advisor (Extens): Chammas & Marcheteau (Nicolas Lecocq, Romain Penloup) 
Legal advisor (Discngine): Lamartine Conseil (Fabien Mauvais, Ahlam Benhamed)
Financing advisor (Discngine): Altman Partners (Jean-Marie Le Tallec, Jean de Limé, Thierry Gauthron) 
 

About Extens
Founded in 2014, Extens Développement e-Santé is a sectoral investment vehicle dedicated to the digital transformation of healthcare. Positioned as a growth fund, Extens invests from €1M to €7M ($1.2-$8.4M) in profitable or nearly profitable companies generating €1M to €20M ($1.2-$23.9M) in revenue with strong growth potential. Its investment targets include: software for hospitals, applications software for healthcare professionals, monitoring solutions for patients at home and health data applications. 
www.extens.fr/en
 

About Discngine
Discngine is a Paris-based software company specializing in applications for the research departments of life sciences companies; specifically for work related to active molecule discovery. It was established in 2004 by two of Pfizer's research alumni in order to develop software that increases the effectiveness of life science research. It currently has 38 employees.
Clients include world leaders in the pharmaceutical, cosmetics and agrochemical industries.
The company's offering has historically been developed around custom software, followed by licenses for software components and most recently by licenses for business solutions. The company will now focus on offering catalog products through SaaS and cloud-based subscription models.
 

Download PDF (English Version)

Download PDF (French Version)

 

Job position - Experienced Full-Stack developer (Oracle, Apex) by Gabriella Jonasson

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Discngine is one of the leading independent life sciences research software integrators and application developers.

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From its inception in 2004 our mantra has been to deliver scientific solutions in order to transform the R&D centers research systems into innovative and intelligent discovery platforms.

Discngine acts as a partner in each phase of the client project, from the design to the delivery of a software solution that supports any research process. Discngine is a dynamic company capitalizing on key skills, rooted in the well-established quality of its consultants.

In order to enforce our R&D team we are hiring a highly-motivated and experienced full-stack developer (Oracle, Apex) who will work in our main offices in Paris (France).

What you will be assigned to

You will join one of our R&D teams developing Disngine's solutions and will take care of:

  • Analysis and edition of technical specifications
  • Applications conception and development
  • Modelling and functional analysis
  • Integration of scientific software packages
  • Integration and non-regression testing
  • Continuous maintenance and correction of applications
  • Documentation, in French and English

The profile we are looking for

You have a Master’s Degree, an Engineering Degree or an equivalent degree in Informatics, and have acquired significative development experience. You are passionate about application development, especially in the Research area. You are proficient in:

  • Relational databases: Oracle Database, PL/SQL, SQL
  • Web development: HTML, CSS, Javascript, REST web services
  • Versioning tools: Git

Knowing the development framework Oracle Application Express can make a difference.

You can efficiently discuss technical aspects in English. 

You are autonomous, you can adapt to different application domains, you are attentive to feedback and you show methodological rigor.

You are willing to embrace the company’s project.

You have nurtured analytical, synthetical skills, and wish to deliver.

You work well with people, and in a team, you favor internal cooperation.

Send us your resume!

Your salary will depend on your profile and experience.

You will be based in Paris, 79 avenue Ledru-Rollin.

You can contact us at jobs _ at _ discngine.com

Meet us for the next ElrigFR event in Monaco, November 27-28th by Grégory Mercier

Check out Discngine Qualification, our novel cloud solution to track and calibrate your liquid handling processes. We will give a demo in collaboration with CyBio at the ELRIGfr Conference in Monte Carlo, Monaco (November 27th).

Make sure not to miss the presentation “Track the accuracy of robotic processes of your pipetting platforms by combining gravimetry and colorimetry data in Discngine Qualification” and discuss directly with Nicolas Alendé.

You want to make sure your instruments are always well calibrated to really trust the assay data they capture for you? Meet us at ELRIGfr!

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Pipeline Pilot in Docker - speeding up complex deployments by Peter Schmidtke

Background

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If you ever had to manage, administer or install a Pipeline Pilot server you know that this is usually not a piece of cake. It's a fairly long process, involves a lot of more or less manual steps (that you could automate, but did you do it so far?).

On top of that...once you have your server installed and everything, it is usually very cumbersome to install a second one, third one fourth one on the same machine to build for instance different dev/test/prod environments, development environments for different people etc...so in the end, most of the time you might have one or two instances of PP on a machine and that's it. 

If you want to clone a particular install (configuration, all packages installed, your own packages installed, users etc...) and maybe a few custom modifications you made to PP then this is also a mainly manual process although Biovia Hub is meant to answer this specific use case I think.

Pipeline Pilot stuffed into Docker

Lately I was spending most of my time on deploying one of our applications that uses Pipeline Pilot on different servers and environments and got a bit fed up with this. So we tried to see whether we could use docker to ease up this whole process for this particular application. Fortunately for you, we also came up with a sufficiently generic docker image for Pipeline Pilot so that various user/administrator profiles could use the image to do very easy and flexible deployments. 

The Pipeline Pilot Image

The image is the thing that holds the Pipeline Pilot install itself. It's the thing that you can pull from a repo or import from a zip file and magically everything is working when launching "docker run". If you use the provided dockerfile to build your image and start the PP container you will notice that this container contains a plain empty install of Pipeline PIlot. Just a few base packages were installed, the server itself and that's it. Nothing is configured on this image yet. 

Now every Pipeline Pilot install is a bit different, the settings are slightly different, user management might be different etc ... this is why we wanted to configure Pipeline Pilot servers at run-time and not build-time, to have a maximum flexibility on deployment. But in the end you are free to do whatever you want.

Another thing is that a docker container always starts in the same state. So in order to run a bunch of PP servers with different settings and packages etc several things had to be adapted around a basic PP installation container. 

Building the Pipeline Pilot 2017R2 Image (tested on Linux)

As I'm not working for BIOVIA I am not allowed to provide you the working docker image as is. So basically you have to build it yourself at your end. Fortunately docker makes things relatively easy. All you need is the attached dockerfile to build the image. All commands in the dockerfile are explained in the file itself and are not further explained in this post. The base image I'm using evolves relatively quickly, but during my last tests all builds were successful.

Place this dockerfile in a folder on a machine where the docker daemon is installed. Then place the Pipeline Pilot installer in the same folder (unzip to the BPP2017R2 folder). Place your pipeline pilot license in this BPP2017R2 folder and name it pp.lic.

Now you can build the pipeline pilot docker image by issuing the following command: 

docker build -t myimagename .

The build will take a quite significant amount of time, but once finished you should have the docker image "myimagename" available when showing all available docker images ("docker images").

Not that the dockerfile can still be optimized, this might follow in an updated blog post. 

The collection data volume

Each flavor of Pipeline Pilot you want to run should have a distinct data volume associated to it. Hereafter I'll refer to this volume as the collection volume.  This volume contains:

  • install.sh (contains the instructions to run when you start the container)
  • pp.lic (the license file of your PP install)
  • config.xml (the PP server configuration, that's the file you can export from your admin portal)
  • DataSource.xmlx (optional) : these are DB data sources defined in the admin portal of a PP server configuration
  • numbered folders containing non-BIOVIA PP collections to install (01_dng_chemistry, 02_dng_network for instance)

The install.sh script provided here installs all custom collections into the apps/discngine folder. You can change that to whatever is suitable for your needs!

To all purists: I know that associating a volume to an image to run a particular instance of software is not the idea of a dockerized application. However, the build process of PP is soooo long, and configuration variety is sooo large that I opted for this as the easiest way to allow a maximum amount of flexibility to the user.

Running a Pipeline Pilot docker image

Once you have built your docker image (or imported it) you can run it using the different flavors of the following command line:

docker run -v collections_dev:/collections -p 9944:9918 -p 9943:9917 ppimagename

You can run another configuration of the same PP server version like this: 

docker run -v collections_prod:/collections -p 9944:9916 -p 9943:9915 ppimagename

and you can do this on the very same server. 

When you run this, the install.sh script will be run and once finished, startserver is run. So if you have 10 big collections to install on startup, this might take a while. Now you can start 3 different servers with the same configuration but different port mappings (-p flag) for instance and deploy different development environments, dev/test/prod environments etc....

Feel free to post comments and suggestions on how to improve the docker image a bit. I know its not perfect yet and probably never will be, but right now it fills a rather pressing need on our side. 

What about user management?

The example provided here does not include any specific user management as this is also very configuration specific. Note that local user accounts are not exported and imported using the PP admin portal tools. Thus they cannot easily be imported via an xml file. However, the install.sh script can easily incorporate sections for local user creation. Basically you can configure your Pipeline Pilot server with the configUtil tool provided by BIOVIA and all of this in the install.sh script. 

If you want to activate LDAP autentication, this could also be done, but you'd need to pass through the hosts /etc/passwd and/or shadow files (on linux) to correctly configure PAM authentication in a docker container for example. There is a lot of documentation on these aspects online (general docker user authentication).

Did you know?

We are already using a little bit more complex example of what was explained above for our 3decision production server. So we already tested a bit the stability of this and were are satisfied.


Downloads

 

Comments or suggestions?

Please use the form below to contact us.

Do more with Spotfire and Pipeline Pilot: the Discngine Connector v4.0 is out! by Claire Wallon

What's new in TIBCO Spotfire Connector for BIOVIA Pipeline Pilot v4.0

TIBCO Spotfire Automation Services integration

You can now to programmatically control the creation, modification, export of a DXP file from the Pipeline Pilot server. Combined with the Pipeline Pilot Data Functions, these new components and automation tasks can prepare new DXP files with dynamic content and deliver them to end-users on-demand or based on schedule.

Real Time Data Synchronization for Spotfire Analyst

When developing Pipeline Pilot workflows for Spotfire Analyst, developers can now activate a real time data synchronization option. When activated, all or a specific list of data tables available in the Spotfire client will be mirrored with a Pipeline Pilot Data cache. This option greatly simplifies the development of advanced workflows where end-users might import and modify data tables on their end.

Release notes
 

A solution for every use case

Job position - Oracle/Web Developer by Thomas Blarre

Discngine is one of the leading independent life sciences research software integrators and application developers.

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From its inception in 2004 our mantra has been to deliver scientific solutions in order to transform the R&D centers research systems into innovative and intelligent discovery platforms.

Discngine acts as a partner in each phase of the client project, from the design to the delivery of a software solution that supports any research process. Discngine is a dynamic company capitalizing on key skills, rooted in the well-established quality of its consultants.

In order to enforce our R&D team we are hiring a highly-motivated web developer with design knowledge who will work in our main offices in Paris (France).

 

What you will be assigned to 

You will join the SCRUM team developing the Sample, Assay and Warehouse solutions (https://www.discngine.com/solutions/) and will take care of:

  • Analysis and edition of technical specifications
  • Applications conception and development
  • Modelling and functional analysis
  • Integration of scientific software packages
  • Integration and non-regression testing
  • Continuous maintenance and correction of applications
  • Documentation, in French and English

The profile we are looking for

You have a Master’s Degree, an Engineering Degree or an equivalent degree in Informatics, and have acquired significative development experience. You are passionate about application development, especially in the Research area. You are proficient in:

  • Relational databases: Oracle Database, PL/SQL, SQL
  • Web development: HTML, CSS, Javascript, REST web services
  • Versioning tools: Git

Knowing the development framework Oracle Application Express (https://apex.oracle.com/en/) can make a difference.

You can efficiently discuss technical aspects in English.

You are autonomous, you can adapt to different application domains, you are attentive to feedback and you show methodological rigour.

You are willing to embrace the company’s project.

You have nurtured analytical, synthetical skills, and wish to deliver.

You work well with people, and in a team, you favour internal cooperation.

Send us your resume!

Your salary will depend on your profile and experience. You will be based in Paris, 79 avenue Ledru-Rollin.

You can contact us at jobs _ at _ discngine.com

Visit us at BioIT World 2017 Conference & Expo in Boston by Eric Le Roux

Join us at BioIT World 2017 Conference & Expo, from May 23rd to May 25th. Take the opportunity to meet our discovery informatics specialists : Dani, Sebastien, Peter and Vincent on booth #121.

Be one the first to try out our new product 3decision®. See https://3decision.discngine.com for more info. A poster will be presented too, an abstract is available here

Get an update on our products for high throughput Discovery (Assay, Sample, Warehouse & Qualifcation) and try them live!

A preview of the newest version (4.0) of our TIBCO Spotfire Connector for BIOVIA Pipeline Pilot will also be available.

On Wednesday 24th, in the Data Computing track, attend to a joint presentation with AbbVie: AIDEAS 3.0: The New Generation Cheminformatics Platform

AIDEAS is an integrated Cheminformatics solution that has brought together several scientific applications and methods under a single umbrella. This presentation will discuss the technology on which AIDEAS 3.0 is built and the scientific application built within AIDEAS 3.0. Examples will be presented to showcase the ability of AIDEAS to provide advanced scientific workflows within one of the best visual analytics frameworks that allows users to share information and define multiple analysis templates in a facile way.
— Rishi Gupta, Senior Research Scientist, Platform Informatics and Knowledge Management, AbbVie, Inc. and Vincent Le Guilloux, Scientific Project Manager, Discngine S.A.S

 

 

Position - Web developer / designer by Daniel Alvarez

Discngine is one of the leading independent life sciences research software integrators and application developers.

From its inception in 2004 our mantra has been to deliver scientific solutions in order to transform the R&D centers research systems into innovative and intelligent discovery platforms.

Discngine acts as a partner in each phase of the client project, from the design to the delivery of a software solution that supports any research process. Discngine is a dynamic company capitalizing on key skills, rooted in the well-established quality of its consultants.

In order to enforce our R&D team we are hiring a highly-motivated web developer with design knowledge who will work in our main offices in Paris (France).

Mission

In an agile development environment you will fulfill the following missions:

  • Be in charge of the front-end development for corporate scientific tools
  • Assist and guide the design of the web app interfaces of all company solutions
  • Participate in the backend development with the rest of the team

Skills

The ideal candidate will have experience using some of these technologies:

  • Strong web development skills using latest technologies: HTML5, angular.js, d3.js, css3, threejs. Cross-browser compatibility issues, user handling, etc.
  • Database development and use: Oracle, SQL & PL/SQL.
  • Linux and Windows environments, ideally at admin level.
  • Scientific software and scientific programming is a plus

Profile

You are an expert web developer using latest technologies with a minimum experience of 2 years working in a professional environment. You develop modern and beautiful web interfaces that grant a good user experience.

You have good communication skills and can expose and understand complex technical problems with ease. You like team work and you’re not afraid of complex environments. Autonomous and curious, you like to take initiatives. You are interested in modern project management methods (agile methods) and novel human resources approaches (reinventing organizations).

Your English is fluent.

Income

35 to 50K€, depending on skills and experience

Apply before

30th April 2017

Contact

jobs _ at _ discngine.com

Forum Labo Paris 2017 by Alexandre Perret

Come visit us at our booth #J35 in Forum Labo 2017 Paris (March 28th to 30th).
We will gladly discuss your projects and demonstrate our solutions for screening, compound management and robotic processes qualification. This year a new version of Discngine Qualification (formerly QPLIMS) will be presented, please find below the preliminary results on the survey we ran in the robotic labs community in partnership with ElrigFr.

 Click for details...

Click for details...

Happy New Year to everybody! Best wishes from Paris! by Eric Le Roux

We wish you all a very successful new year!

This year our greeting card is introducing a brand new field of activity for discngine. Structural bioinformatics, knowledge management and decision making will be integrative parts of a new product launched early 2017 called 3decision. We aim to introduce a complete paradigm shift on structural analytics and visualization to rapidly shape a new way of handling structural information and knowledge in the public and private domain!

Keep yourself updated on the product launch and all exciting news about our other products by following us on twitter linkedin

Greeting Card 2017

 

And as usual, find below all greeting cards from the inception of discngine till today!