Web interface provided on SQLMOL

A simple web interface is provided on SQLMOL now. It is writen in ASP.NET and jQuery is used from Google’s code hosting. The molecule structure images are generated by the Daylight‘s SMI2GIF service. SMI2GIF is so excellent that it can not only transform your SMILES to structure image but also highlight the substructure you have queried.

As SQLMOL is currently only implemented on SQL Server, you should have a MS Windows enviorenment to run it. Then I recommend the free tool Visual Web Developer to handle the source file and run the code to test.

SQLMOL is so simple and light weight substructure search system that can deployed on a common PC in half-an-hour. Just try it.

 

Mind Map of ITIL v3

The original content is created by the blog ITIL SERVICE MANAGEMENT on the post ITIL V3 Mind Map Download OCT 7, 2007. The author has moved the MindManager file to google pages and is downloadable following the post’s comments.

This MindManger has a filename extension of mmap. I imported it to the free mind map software FreeMind ( there’s a portable version at http://portableapps.com/node/6903) and FreeMind is so powerful to export the mindmap into a feature rich flash format. You can find it on my site, follow the link and enjoy.

http://charliezhu.com/itil/ITILV3.mmap48083.html

Cross tabulation, Pivot table and OLAP Cube summarized by tools

Cross tab

Cross tabulation , is defined on WikiPedia as A cross tabulation (often abbreviated as cross tab) displays the joint distribution of two or more variables.

As below figures, the column values of the first table is transformed to column names in the second one, so the production of

 

 

Cross tabs are frequently used because:

  1. They are easy to understand. They appeal to people who do not want to use more sophisticated measures.
  2. They can be used with any level of data: nominal, ordinal, interval, or ratio - cross tabs treat all data as if it is nominal.
  3. A table can provide greater insight than single statistics.
  4. It solves the problem of empty or sparse cells.
  5. They are simple to conduct.

 

I think the cross-tab is really what the Relational Database means. That’s a meaningful “Relationships” between entities but not entity and it’s attributes.

Solution by SQL Server 2005

Code:

SELECT
    SalesPerson,
    [Oranges] AS Oranges,
    [Pickles] AS Pickles
FROM
    ( SELECT SalesPerson, Product, SalesAmount FROM tblSales ) ps
PIVOT
    (
      SUM (SalesAmount)
      FOR Product IN ( [Oranges], [Pickles])
    ) AS pvt

 

This most weak part of feature is that you must list all pivot column name manually. It’s pain.


BOL: Using PIVOT and UNPIVOT

SELECT < non-pivoted column>,
    [first pivoted column] AS ,
    [second pivoted column] AS ,
    ...
    [last pivoted column] AS
FROM
    (< SELECT query that produces the data>)
    AS
PIVOT
(
    < aggregation function>()
FOR
[< column that contains the values that will become column headers>]
    IN ( [first pivoted column], [second pivoted column],
    ... [last pivoted column])
) AS
< optional ORDER BY clause>;

Solution by MS Access

Microsoft Access provides a very nice cross table design wizard.

With the wizard, we get the cross-tab script based on JET-SQL.

TRANSFORM Sum(tblSales.SalesAmount) AS [Sum of SalesAmount]
SELECT tblSales.SalesPerson, Sum(tblSales.SalesAmount) AS [Total SalesAmount]
FROM tblSales
GROUP BY tblSales.SalesPerson
PIVOT tblSales.Product;

 

 

Pivot columns is automaticly generated and the aggregation over all pivot column can be produced. The JET-SQL is so smart and smoothly for small applications those don’t have to be scaled. You can use almost all VBA programming utilities in it. The TRANSFORM/PIVOT feature is powerful and more then 5 years before the SQL Server’s implementation.

It is based on JET-SQL, so not availible in an ADP project.

Solution by SQL Server 2000, CASE and GROUP

The classic solution of cross-tab in SQL Server 2000 or before is produced by CASE and GROUP.

select
    SalesPerson,
    SUM(CASE Product WHEN 'Pickles' THEN SalesAmount ELSE 0 END ) as [Pickles],
    SUM(CASE Product WHEN 'Oranges' THEN SalesAmount ELSE 0 END ) as [Oranges],
    SUM(SalesAmount)    as [Total Sales]
from
    tblSales
group by
    SalesPerson

We can find it’s footprint clearly in the SQL Server 2005’s pivot feature. And this is a base for other ideas.

Solution by SQL Server 2000, Dynamic SQL

Dynamic Cross-Tabs/Pivot Tables By Rob Volk

The basic idea is to generate dynamic CASE-and-GROUP based SQL statement and execute.

The following comments providing many improvement on this solution. i.e.

  • Introduce an WHERE statement as parameter for the @PivotColTable.
  • Using string to generate pivot columns but global temp table for better supporting of concurency calling.
  • Using user defined table with an user session column instead of global temp table.
  • To summarize multiple values.

There is also an similar solution I have not dived in, Dynamic Crosstab Queries, by Itzik Ben-Gan .

Solution by Excel

But the most easy and rich tool I have used is MS Excel’s pivot table.

Pivot table and OLAP Cube

The basic idea of OLAP Cube is a multi-dimession pivot table. The common visualization tool for OLAP is also a pivot table or pivot chart viewer. 

So, draw a figure to show basic concepts in OLAP by example metioned above as the END.

Implementing Slope-One in T-SQL

Slope-One, the simplest form of non-trivial item-based collaborative filtering based on ratings. (Original Paper)
Referencing to Bryan O’Sullivan’s tutorial of implementing Slope One in Python, I write a the implementation in T-SQL. Believe it useful to many people and projects.

Brief process summary

  • Define the fact table as user data.
  • Calculating intermediate matrix(FreqDiff). The information about users is eliminated and frequency/ score differences data between items is produced.
  • Predicting from user input score with the intermediate data.

Data schema

The UserData is fact table of business transactions. I use an view to wrap it for switching between testing data and working data.
The Freq&Diff matrix is square and sparse. Only non-zero values is meaningful and stored. And a half-matrix triangle holds full information about the matrix.
There created two indices to avoid heavily bookmark-lookup.

create table UserData (                  -- fact table
    userid   varchar(50) not null,
    itemid   varchar(50) not null,
    rating   float not null default 0,
    updtime  datetime default getdate(),
    primary key (userid, itemid)
)
GO

create table FreqDiff (                  -- Freqs and Diffs
    itemid1  varchar(50),
    itemid2  varchar(50),
    freq     float not null default 0,
    diff     float not null default 0,
    updtime  datetime default getdate(),
    primary key (itemid1, itemid2)
)
GO
create index idx_freqdiff_itemid1 on FreqDiff(itemid1, freq, diff, itemid2)
create index idx_freqdiff_itemid2 on FreqDiff(itemid2, freq, diff, itemid1)

/*
 * The matrix FreqDiff is *almost* symmetric,
 * so only half of the data need to be stored.
 * There would be huge of space (50%) saved for large dataset.
 */
alter view vw_freqdiff as
select itemid1 as itemid1, itemid2 as itemid2, freq,     diff from FreqDiff fd
union all
select itemid2 as itemid1, itemid1 as itemid2, freq, -1* diff from FreqDiff fd
GO

/*
 * Wrap for userdata,
 * switch from one model to another easily.
 */
alter view vw_userdata as
select * from userdata
GO

Testing data

Same as Bryan’s but names changed for easily debugging print.

-- init userdata, Bryan O'Sullivan's sample data is used
insert into UserData values ( 'u1', 'i1',  1, getdate() )
insert into UserData values ( 'u1', 'i2', .5, getdate() )
insert into UserData values ( 'u1', 'i3', .2, getdate() )
insert into UserData values ( 'u2', 'i1',  1, getdate() )
insert into UserData values ( 'u2', 'i3', .5, getdate() )
insert into UserData values ( 'u2', 'i4', .2, getdate() )
insert into UserData values ( 'u3', 'i1', .2, getdate() )
insert into UserData values ( 'u3', 'i2', .4, getdate() )
insert into UserData values ( 'u3', 'i3',  1, getdate() )
insert into UserData values ( 'u3', 'i4', .4, getdate() )
insert into UserData values ( 'u4', 'i2', .9, getdate() )
insert into UserData values ( 'u4', 'i3', .4, getdate() )
insert into UserData values ( 'u4', 'i4', .5, getdate() )
GO

Processing the intermediate table

-- update process
delete FreqDiff
insert into FreqDiff
select
    ud1.itemid, ud2.itemid, count(*), (sum(ud1.rating - ud2.rating))/count(*), getdate()
from
    vw_userdata ud1
    join vw_userdata ud2 on
            ud1.userid = ud2.userid
        and ud1.itemid > ud2.itemid
group by ud1.itemid, ud2.itemid

Predicting

-- predict process
declare @pref table(itemid varchar(50), rating float)
insert into @pref values('i1', 0.4)

select -- distinct top 10
    itemid1,
    sum(freq)                               as freq,
    sum(freq*(diff + rating))            as pref,
    sum(freq*(diff + rating)) /sum(freq) as rating
from
    vw_freqdiff fd
    join @pref p on fd.itemid2 = p.itemid
where itemid1 not in( select itemid from @pref )
group by itemid1

Further works as intermediate data updating seems easy.
So, writing here, listening for suggestions.

Config VirtualBox with Host Interface Networking (HIF)

Diagram as the note.

Config VirtualBox with Host Interface Networking (HIF)

Structure searching supported compound database based on MS Access




Why based on MS Access

MS Access is wildly used, easily available and almost the most user friendly database product. I know many stuffs are working on MS Excel for compound information management and there exists such commercial solutions, the reasons coincide.

The solution described here is for

  • Small account of products catalog.
  • Fast development needed.
  • User interface and operation are crucial, or chemical information data is trivial part of the database.

Demonstration of functions


Platform and tools used

Solution step by step

  • Sample data

SDF files are downloaded directly from Pubchem ftp, it’s free and public.

  • Import SDF file into Access

As the structure description part (mol file) exists inside each compound, it’s not easy to parse the SDF file to csv and other table based format. I write a simple Python script to transform SDF file to Access accepted XML file. You can create a desired table in Access database and export it to XML format to get the XML template.

When data are ready, just run import command from Access.

You can also try RDkit to manipuate SDF and structure information in Python, it’s professional.

  • Generation of structure pictures

When transforming SDF file with Python, some further more actions be taken to generate BMP structure pictures.

Use Molconvert to convert the mol file into PNG format

os.system( “molconvert png %s/%s.mol -o %s/%s.png” %(folder, molid, folder, molid) )

Use PIL to convert PNG to BMP

Image.open( “%s/%s.png”%(folder, molid)).save(”%s/%s.bmp”%(folder,molid))

BMP pictures are needed because native Access only accepts BMP picture as OLE object and displayed on form control.

  • Embed Ole object with VBA

Public Sub load_img()
Me.Recordset.MoveFirst
While Not Me.Recordset.EOF
Me.pic.OLETypeAllowed = acOLELinked
Me.pic.SourceDoc = CurrentProject.Path & “img” & Me.cid & “.bmp”
Me.pic.Action = acOLECreateLink
Me.pic.SizeMode = acOLESizeStretch
Me.Recordset.MoveNext
Wend
End Sub

  • JME as structure query input

JME is a java package and I don’t know any way to combine it with Access directly. So an webcontrol is introduced to the Access form and JME embedded on the source page of the webcontrol. The dom object visit is more simple than I had imaged.

mol = Me.WebBrowser2.Document.applets.Item(0).MolFile()

  • Implentation of sturcture search function

This is truely the key technic of the solution. It is powered by opensourced checkmol/machmol. Acturally, just after read the usage part of source code of its dll version, I begun to think about to do something on Access. Access database uses JETSQL engine, it’s not as powerful as T-SQL, but it supports VBA functions. VBA code can easily visit exernal dll function, so JETSQL could be extended greatly.

So, the sturcture search code is really simple


select * from sample_data where MatchMol(query_mol, mol) > 0


MatchMol function is pre-defined by dll apis of checkmol/matchmol.

Code copied from MATCHMOLDLL.pas

——————————————————————————–
Private Declare Sub mm_SetMol Lib “matchmolDLL.dll” (ByVal st As String)
Private Declare Sub mm_SetCurrentMolAsQuery Lib “matchmolDLL.dll” ()
Private Declare Function mm_Match Lib “matchmolDLL.dll” (ByVal Exact As Boolean) As Long

Private Declare Function mm_GetRings Lib “matchmolDLL.dll” () As Long
Private Declare Function mm_GetAtomRing Lib “matchmolDLL.dll” (ByVal AtomNumber As Long) As Long
Private Declare Sub mm_Version Lib “matchmolDLL.dll” (ByVal st As String)

Public Function MatchMol(Needle As String, Haystack As String, Optional ExactMatch As Boolean = False) As Boolean
Static oldNeedle As String
If oldNeedle <> Needle Then
oldNeedle = Needle
mm_SetMol Needle
mm_SetCurrentMolAsQuery
End If

mm_SetMol Haystack
If mm_Match(ExactMatch) <> 0 Then MatchMol = True

End Function
——————————————————————————–

Performance issues

As a small database, there are about 2700 compounds are imported.

  • Ole picture in BMP format consumes much space. The database file size grows to 600MB.
  • Substructure searching is too fast to recognize delay.
  • If function group or fingerprint is introduced as database index, the substructure searching could archive great performance on large scale dataset.
  • The data importing process is slow and the structure pictures generation process costs much more time and CPU. It took about half an hour to convert the 2700 BMP files on my thinkpad.

Other References


Appendix 1

Such Access DB can NOT serves for Asp.net or other applications connect through ODBC/DAO, for “ODBC and DAO do not use or know anything about the code modules inserted into an .mdb file by Access. Only Access recognizes the modules. ” announced by MSDN KB [Q166113] You cannot use user-defined modules through ODBC or DAO.

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