Egis Pharmaceuticals PLC, Budapest, Hungary, developed a chemical database for 20 years based on at first MDL’s ChemBase then later ISIS/Base. The database included both chemical and biological data and served Egis’ chemistry and biological community of 74 users. With emerging internal demand for a change ChemAxon’s JChem platform and ComCix’s integration and workflow framework were selected as the next generation integrated solution. During the project we faced usual and expected difficulties but also some unforeseen challenges caused by for instance the different project management methods of the two companies or heterogeneous data sources requiring major data clean up processes, and most importantly the acceptance of the new system by the user community that was accustomed to their legacy system. In our joint presentation we are going to show some of these challenges from two different aspects: one from the costumer and the other from the integration provider.

1. 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
EGIS

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)
 Easy Reaction Handling and Project
Parameter Management
 Automatic Calculation of Input
Quantities
 Paralel synthesis module
Electronic Laboratory Notebook
Easy upload and filter of reactions and project
parameters
 Inventory Management of Starting
Materials and Reagents
 Building Blocks with Inventory Data
 Complete tracking of reagent usage
 MSDS Upload
Reagent inventory
User Friendly Solution for Stock Records
Product Inventory
Management of orders
e-Procurement
High-level information on
project progress, status
Material cost and
worktime (timesheet)
registration
Management
Easily manageable analytical
database, analytical devices
can be connected online
Central Analytical Module
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. ..
collective databases
SCREEN databases
..
EgisAkt
safety copies
EgisAkt
Preparative Laboratory databases
C_DbSave
Structure-Activity selections
3D databases
BioReForm
Osiris
DAtf32
Spectroscopic databases
..
Assign MScorp
, ,
NMRtf NMRsend
Notations:
ISIS database FoxPro database
program
ACD, Cassandra
plans
EGIS

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)