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

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

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 StartingMaterials 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 ModuleTracking and Inventory Management of Final Products

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

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

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

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

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

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

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

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

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

The Kamilla system

Three moduls were rolled out

reagent inventory

ELN module

analytical module

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

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

Egis before the migration

• 20 years with MDL softwares (ChemBase,

ISIS)

• Chemical and biological data

• Chemical structures and reactions

• 74 users

..

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

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

Results of the migration

• About 90 % of data were migrated without

problems

• 10 %:

- Old undetected errors

- Different philosophy about integrity

- Stereochemistry

Stereochemical problems 1 (central chirality)

Stereochemical problems 2 (axial chirality)

Stereochemical problems 3 (planar chirality)

Stereochemical problems 4 (helical chirality)

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?

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.

Tagetes patula (French marigold)