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!

qualification.PNG
elrig.png

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

SAM-PlateDetails2.png

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

plate_statistics_full_screen.png

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

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

Background

dockerPP.png

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.

SAW_V3.5.2_Assay_Well Validation.PNG

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!

Spice up your TIBCO Spotfire documents with the new release 3.4 of the Pipeline Pilot Connector by Claire Wallon

This new release is compatible with TIBCO Spotfire 7.6 and Pipeline Pilot 2017

What's New in 3.4

TIBCO Spotfire Web Player Composite Mashup

Combine Pipeline Pilot report elements and Spotfire Visual Analytics elements in a single page (requires Spotfire 7.5+)

New Registration interface for Pipeline Pilot Data Functions

Registered data functions can be browse through the Spotfire Library representation or the Pipeline PIlot XMLDB representation

Improved SBDF Reader/Writer

Date and Time format are now supported

 

See live demos at the Spotfire European User Group meeting

Discngine will present the latest version of the connector during the "2016 Data Analytics & R&D Informatics User Conference"

The 2016 Data Analysis and R&D Informatics User Conferences have been designed to offer insights and value for the full breadth of the TIBCO Spotfire® community – from Academia, Industry, Business Managers, and IT professionals. We have an exciting line up of Speakers, case studies, interactive demos and networking opportunities.

Hear how industry leaders are using TIBCO Spotfire® software to build robust enterprise solutions to speed up Research and leverage the full potential of their experiments.

Don’t miss your chance to meet industry leaders, your peers and take away key learnings and TIBCO Spotfire® skills that will change the way your data looks forever.

Discngine - Sponsor of the upcoming German Conference on Chemoinformatics by Peter Schmidtke

 

We decided to reiterate our support to the German Conference on Chemoinformatics to be held in Fulda in November this year. 

You will have the chance to meet Daniel Alvarez-Garcia and myself at our booth and learn more about our TIBCO Spotfire Connector for BIOVIA Pipeline Pilot, the Pipeline Pilot Component Collections or our latest developments on Sample & Assay. In case you are very insisting, we will also present you a few things about our very exciting R&D pipeline of products to be launched in 2017.

Also make sure to attend my talk on Monday 7th November at 11:40am entitled "Practices in Structure Based Drug Design: A Huge Waste of Resources?". In this perspective I'll resume current practices and trends in structure based drug design to handle experimentally resolved structures and their derived information. I will particularly focus on the obstacles to achieve a good return on investment, discussing near future perspectives and solutions.

Last but not least, we also bring our PhD Student Nicolas Shinada with us and he will present a poster on very, very early results entitled "Beyond the classical view of molecular interactions in protein-ligand recognition". Make sure to stop by his poster and challenge him a bit!

Looking forward meeting you in Fulda!

 

4th Discngine internal Agile development summit by Ariane Allain

Last week, was held in Paris the 4th Discngine internal Agile development summit. On Tuesday and Wednesday 11-12 of July, our Agile coach Claude Aubry gathered together the enthusiastic Discngine developers in the heart of Paris for a two-day dive into the inner working of SCRUM.
Through Flapex, a fictive home-made application, we experimented the whole life cycle of a SCRUM team. As usual, Claude alternated presentations with fun games and workshops to sharpen our SCRUM skills. To give you a taste of our agenda, we tackled release, sprint, planning, story mapping, story refinement, review, retrospectives…
Thanks to Claude for being one more time such a great SCRUM half !
Thanks to the team Agile Tribu for hosting us in their premises at a stone’s throw from our new Parisian offices in Avenue Ledru-Rollin !

 

 

Discngine sponsor of the Chemoinformatics Summer School 2016 in Strasbourg by Alexandre Perret

For the first time, Discngine sponsors the Chemoinformatics Summer School in Strasbourg (CS3). Nicolas Shinada, Daniel Alvarez Garcia, Vincent Le Guilloux and Alexandre Perret take the opportunity to give a 2-hour workshop on how to conduct chemoinformatics research with BIOVIA Pipeline Pilot by using the BIOVIA and Discngine Chemistry Collections.

In this event, Daniel Alvarez Garcia will also present the last advances in a Discngine internal research project.

Come to visit us at our booth to get more information about the different projects at Discngine !

Meet us at booth #1 at the BIOVIA event in Boston on May 23rd to May 26th by Eric Le Roux

Discngine silver sponsor of  the BIOVIA event "Science In The Age Of Experience 2016"

It will be a nice opportunity to try out our applications and discuss with our CSO Peter Schmidtke, PhD and myself.

The latest versions of our collections for Pipeline Pilot (TIBCO Spotfire connector, Chemistry and Network) will be presented as well as our suite of data centric solutions for high throughput research: "Sample", "Assay", "Warehouse" and the future product "Workflow". Rendez-vous at booth #1 for demos.

"Sample" and "Assay" will be also available in the BIOVIA Product Gallery area (Playground).

I will present our recommended approach for software integration in the track "Collaborative Science in Life Sciences Research" on Wednesday 26th at 1:45PM.

Discngine solutions for Researchers:

Connect TIBCO Spotfire 7.5 with BIOVIA Pipeline Pilot 2016 by Vincent Le Guilloux

This new minor release (3.3) ensures compatibility with the latest versions of TIBCO Spotfire (7.5) and BIOVIA Pipeline Pilot (2016)

What's new

Compatibility

TIBCO Spotfire 7.5 is now supported.
BIOVIA Pipeline Pilot 2016 is now supported.

New sub-menu for the Discngine Web Panel tool

The sub-menu of the Discngine Web Panel tool exposes two options: new document creation and home page resetting

Minor changes and bugs fixed

Fixed bugs due to changes in TIBCO Spotfire 7.0+ panel management system

Multi Data Functions execution in a TIBCO Spotfire document

See it live!

BIOVIA SCIENCE IN THE AGE OF EXPERIENCE

MAY 23-27, 2016 | BOSTON, MA

BIOVIA FORUM 2016

6 – 9 JUNE 2016 | NOORDWIJK AAN ZEE | THE NETHERLANDS


Download

ftp.discngine.com

 

 

DISCOVER THE LATEST VERSIONS OF ASSAY & SAMPLE LAUNCHED AT THE NEXT ELRIGfr EVENT ! by Alexandre Perret

 

This year, Discngine sponsors the ELRIGfr event on Lab Automation, Formulation and Phenotypic Screening. Jean-Philippe Laval, Fabrice Casagrande and myself (Alexandre) will be happy to welcome you at booth #8 to show you the latest versions of our Assay & Sample products.

Discngine Assay Screenshot

Discngine Sample Screenshot

Also, make sure to assist our snapshot session on Tuesday 3rd, afternoon for the launch of Sample & Assay.

Looking forward to seeing you there. 

New release (3.2) of the TIBCO Spotfire Connector for Pipeline Pilot by Eric Le Roux

We are pleased to announce the availability of the version 3.2 of the Discngine TIBCO Spotfire connector for BIOVIA Pipeline Pilot!

Faster Direct Data Upload to Pipeline Pilot server
The Discngine TIBCO Spotfire Connector for Pipeline Pilot v3.2 improves considerably the
“TIBCO Spotfire Upload Data Table” Pipeline Pilot component. This component allows users
to upload TIBCO Spotfire data directly to the Pipeline Pilot server. This component has been
rebuilt and now it uses a new Pipeline Pilot API that allows improving the performance of this
method.

Pipeline Pilot Data functions Security and Data Caching
Data Functions are now storing your Pipeline Pilot Session ID in a different manner, which
facilitates the security and reuse of this session ID. Session ID is now stored in the user
preferences and it is not dependent on the TIBCO Spotfire document. However, changes are
keeping backwards compatibility with old TIBCO Spotfire Documents that were using
previous saving method.
In the WebPlayer context, users can now authenticate against the Pipeline Pilot server.Data Function result set cache is now controlled at registration time.

Pipeline Pilot authentication form in Spotfire Web Player

Pipeline Pilot authentication form in Spotfire Web Player

Improved Javascript API Documentation
The javascript API comes with an improved documentation that allows users to navigate
through easily and find the right information quicker.