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[Joelib-devel] JOELib/JOELib2 differences: Why do we need more engineering in Cheminformatics
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From: Joerg K. W. <we...@in...> - 2005-05-12 10:05:50
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Hi,
three main differences:
1. JOELib2 contains a better class and interface structure. Which means,
external developers find a more stable cheminformatics interface. And
the probability to change the interface the next two years was reduced.
Of course, there are a lot of possible improvements possible, especially
to improve the pre-screening and speed of the query matching, but this
should now not affect the basic interface for external users. This will
be the next big refactoring, which should be adressed. Until now I am
still really busy with writing at my thesis, so I have no time for that,
but comes time comes thesis comes (hopefully) time :-)
2. The source code was cleaned up and the bug hunting for the underlying
chemical expert system is now easier in JOElib2 than before. Thats what
software engineering means. Combine practical engineering knowledge for
users with scientific standards, here chemical expert systems. But we
need more documentation, documentation, and documentation AND
*automatic* testing, testing, and testing, especially for the chemical
expert system, which contains very often ambigious or contradictionary
feature calculation methods.
3. Better algorithm development possibilities. My main working field is
method based cheminformatics development and fast algorithm prottyping
for mining tasks. So, JOELib fullfills those requirements, analogue to
MATLAB. If you need real speed you can transform the gained algorithm
knowledge to develop faster, but larger programs and processor optimized
algorithms.
BTW, there is a study the the main costs are not the development costs,
but the maintenance costs. So, the maintenance and future developments
cause 2/3 of all costs, so it is highly recommended to make such re-designs.
Especially in cheminformatics and drug design, where we have a lot of
expert knowledge it is highly recommended to combine the knowledge and
the engineering tasks in IT.
Kind regards, Joerg
> Hi
>
> Thank you very much.I am new to list and to use
> joelib.And one more thing is not clear to me what is
> the difference between joelib and joelib2?
>
> Thank you in advance
>
> Regards
>
> Deepak
>
>
>
> --- "Joerg K. Wegner"
> <we...@in...> wrote:
>
>
>>You should use Java1.5 for JOELib2 (still alpha, but
>>recommended)
>>
>>or use the old JOELib version, which is Java1.4
>>
>>Kind regards, Joerg
>>
>>
>>>Hi
>>>I have problem building joelib from the source.The
>>>build process stop at compile.core saying.im using
>>>recent joelib download,ant on xp
>>
>>
>>
>>>
>>
>>
>>
>>>compile.core:
>>
>>
>>
>>> [echo] Compiling
>>
>>core
>>
>>>JOELib2-alpha library.
>>
>>
>>
>>> [javac] Compiling 856 source files to
>>>D:\JOELib2-alpha-20050303\build [javac]
>>>javac: invalid target release: 1.5
>>
>>
>>
>>> [javac] Usage: javac <options>
>>><source files>
>>>[javac] where possible options include:
>>
>>
>>
>>> [javac] -g
>>
>>
>>
>>> Generate all debugging info
>>>[javac] -g:none Generate no
>>>debugging info [javac]
>>>-g:{lines,vars,source} Generate only some
>>
>>debugging
>>
>>>info [javac] -nowarn
>>>Generate no warnings
>>
>>[javac]
>>
>>>-verbose Output messages about
>>
>>what
>>
>>>the compiler is doing
>>
>>
>>
>>> [javac]
>>
>>>-deprecation Output source locations
>>>where deprecated APIs are used
>>
>>
>>
>>>
>>
>>[javac]
>>
>>>-classpath <path> Specify where to find
>>
>>user
>>
>>>class files [javac] -sourcepath <path>
>>
>>
>>
>>>Specify where to find input source files
>>
>>
>>
>>>
>>
>>
>>
>>> [javac] -bootclasspath <path>
>>>Override location of bootstrap class files
>>
>>
>>
>>>
>>
>>
>>
>>> [javac] -extdirs <dirs>
>>>Override location of installed extensions
>>
>>
>>
>>>
>>
>>
>>
>>> [javac] -d <directory>
>>>Specify where to place generated class files
>>
>>
>>
>>>
>>
>>
>>
>>> [javac] -encoding <encoding>
>>>Specify character encoding used by source files
>>
>>
>>
>>>
>>
>>
>>
>>> [javac] -source <release>
>>>Provide source compatibility with specified
>>
>>release
>>
>>>
>>
>>
>>
>>> [javac] -target <release>
>>>Generate class files for specific VM version
>>
>>
>>
>>>
>>
>>
>>
>>> [javac] -help
>>>Print a synopsis of standard options
>>
>>
>>
>>>
>>
>>
>>
>>>
>>
>>
>>
>>> Any suggestion
>>
>>highly
>>
>>>appreciated
>>>
>>>Regards
>>>
>>>Deepak
>>>
>>>
>>
> ________________________________________________________________________
>
>>>Yahoo! India Matrimony: Find your life partner
>>
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>>
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>>>
>>>
>>>
>>
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>
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>>
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>
>>
>>--
>>Dipl. Chem. Joerg K. Wegner
>>Center of Bioinformatics Tuebingen (ZBIT)
>>Department of Computer Architecture
>>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
>>Phone: (+49/0) 7071 29 78970
>>Fax: (+49/0) 7071 29 5091
>>E-Mail: mailto:we...@in...
>>WWW: http://www-ra.informatik.uni-tuebingen.de
>>--
>>Never mistake motion for action.
>> (E. Hemingway)
>>
>>Never mistake action for meaningful action.
>> (Hugo Kubinyi,2004)
>>
>>
>
>
>
> ________________________________________________________________________
> Yahoo! India Matrimony: Find your life partner online
> Go to: http://yahoo.shaadi.com/india-matrimony
>
--
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
(E. Hemingway)
Never mistake action for meaningful action.
(Hugo Kubinyi,2004)
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