TWO SIDES OF A MIGRATION PROCESS

Transcription

1 EGIS TWO SIDES OF A MIGRATION PROCESS Tamás Nagy (Egis), András Dancsó (Egis), László Vágó (Egis), Balázs Volk (Egis), Gábor Pőcze (ComCix), Ferenc Darvas (ComCix) ChemAxon EUGM 2015

2 Kamilla: the choice for your life science research Kamilla: Adaptation of the all-purpose, multiface system Laboratory Manager Plus for supporting research at EGIS Project participants EGIS pharmaceutical company ComCIX (Institute of Innovation): Innovation development arm of Darholding Network, Central Europe s largest upstream technology holding with corporations in HU, US, UK, IR. Focal points: drug and agrochemistry discovery and nanotechology, flow chemistry, microfluidics, clean technology. IT is based mainly on ChemAxon software

3 Laboratory Manager Plus overview (basic concept of Kamilla) Electronic Laboratory Notebook Easy upload and filter of reactions and project parameters Easy Reaction Handling and Project Parameter Management Automatic Calculation of Input Quantities Paralel synthesis module Reagent inventory User Friendly Solution for Stock Records Inventory Management of Starting Materials and Reagents Building Blocks with Inventory Data Complete tracking of reagent usage MSDS Upload e-procurement Management of orders Management High-level information on project progress, status Material cost and worktime (timesheet) registration Central Analytical Module Easily manageable analytical database, analytical devices can be connected online Product Inventory Tracking and Inventory Management of Final Products

4 Background: applications beyond Kamilla Background development started in 1996 for ComGenex, Europe s first Combinatorical Chemistry Corporations Fully developed version 2003 approx 100 chemist users and over 10 discovery laboratories 2 locations, remote users from Germany and US Development restarted in 2012 applications extended to flow chemistry/microfluidics and nanotechnology ThalesNano (30 users) flow chemistry project management, timecards NanGenex, nanotechnology (20 users) project management hts screening plate based workflows and visualization ComInnex, CRO (30-40 users) chemistry and analytics barcoding, android tlc application instrument integration, result storage, project management, profitability of projects

5 Kamilla Project Key requirements data stored in legacy system have to be migrated into the new system molecules, reactions, physical property data, biological data more than 150 different fields support EGIS workflows reagent handling analytical sample handling, LCMS, NMR, Elemental Analysis, etc. reports analytical request and result pages chemical synthesis reports (ELN) barcode handling Hungarian language support Why ComCIX was chosen 2 similar systems (ComInnex, NanGenex) sound positive feedback from existing users experience with ChemAxon toolkits chemical development workflows existing framework (Laboratory Manager Plus) to support fast development

6 Laboratory Manager Plus framework Core functions Chemical database Research workflow support system built in ChemAxon toolkit Database structure for the basic tasks molecule insert, update, delete reaction insert, update, delete structure based filters and searches Tools for web GUI building Box/Record/Filter/Tree views simple report handler simple exporter html, txt, xls, sdf formats Role based authentication system Project based authentication system

7 Laboratory Manager Plus framework (GUI) Record view Basic GUI tool of the system Used for most data visualization Has two main forms: record and chart view. The chart view allows the handling of multiple records and gives an easy overview Subforms are supported Operators for searching, filtering. Structure as data type insert, update, delete search (sub)structure Automatic list handling list logic supported union, intersection, etc... search results are stored as lists

8 Laboratory Manager Plus framework (GUI) The filter view is the central part of each workflow Two sections: filter and result The results can be grouped by any visible fields Operations with the records can easily be defined

9 Laboratory Manager Plus framework (GUI) Box view: Support for column and row based visualization Operations with the records can be defined easily insert, move, new items As set up only properties need to be edited

10 Laboratory Manager Plus framework (GUI) Tree view (project based visualization) two different versions: tree (library syntheses) and reaction pathway alternate routes can be created and selected easy data manipulation: insert reaction, set up reaction set up multiple reactions

11 Challenges during implementation of Kamilla Hungarian language support original framework in English multilingual support mysql procedures, java programs, html templates, javascript codes Data migration from legacy data heterogeneous data source ISIS db, MS sql, text, pdf files numerous data clean up numerous duplicate filtering caused by Hungarian characters extensive use of ChemAxon API extensive programming and testing every test round brought up new errors actual process took 3-4 hours had to be restarted 3 times finally successful

12 Project management and timeframe The timeframe was 9 month EGIS preferred linear project management ComCIX supported agile like project management with short development cycles Agreed project setup Creation of extensive functional specification Setup of a test system at the start so that framework and new functions could be tested Weekly/Biweekly meetings new functions/forms/reports were rolled out to the test system for test and feedback new ideas were discussed Production ready Laboratory Manager Plus framework distributed to all systems if altered

13 The Kamilla system Three moduls were rolled out reagent inventory ELN module analytical module

14 User s feedback Like: integrated solution easy to search, simple data mining reports (ELN, analytics) project based statistics worklow support Don t like: browser based bugs drawing tool is not completely ISIS like + Java applet delays tree view doesn t support multiple reaction paths error correction is complicated

15 Chemaxon tools Tools used during the project JChem Base structure was defined as data type in Laboratory Manager Plus sss in background thread Calculator plugins svg charts were developed robust API resulted in shorter programs Instant JChem used only during migration for data clean up easy to use for simple tasks, scripting is not so simple Marvin applets lots of problems because of Java, browser Marvin JS easy to integrate

16 Egis before the migration 20 years with MDL softwares (ChemBase, ISIS) Chemical and biological data Chemical structures and reactions 74 users

17 EGIS collective databases.. EgisAkt SCREEN databases ACD, Cassandra DAtf32 EgisAkt safety copies.. plans Preparative Laboratory databases C_DbSave BioReForm Structure-Activity selections Osiris NMRtf NMRsend 3D databases Spectroscopic databases Assign MScorp..,, Notations: ISIS database program FoxPro database

18 Preparing the migration Why to leave ISIS? Requirements: - Client-server architecture - Compatibility with newer Windowses - Web-based user interface - Integrated system, support of workflows - Forms, reports Why ChemAxon? Integrator: ComCix

19 Results of the migration About 90 % of data were migrated without problems 10 %: - Old undetected errors - Different philosophy about integrity - Stereochemistry

20 Stereochemical problems 1 (central chirality)

21 Stereochemical problems 2 (axial chirality)

22 Stereochemical problems 3 (planar chirality)

23 Stereochemical problems 4 (helical chirality)

24 Other problems Java + safety policy = Browsers with different behaviors When the integrator is faced existing logical inconsistencies, which is better: - support them in the program or - reorganize workflows?

25 Users Which kind of users has to be a system planned for? What is the most effective training? Chemists are usually intelligent people, but not necessary computer gurus To make the tests.

26 Tagetes patula (French marigold)