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PipeWorkReferenceManual describes each PipeWork provided by Genoret Database

Contents 1 General behaviour 2 General purpose tools 2.1 PasteToHtmlTable 3 GO PipeWork Reference Manual 3.1 Go 4 GX PipeWork Reference Manual 4.1 GXRatio 4.2 GXSamples 5 =GxManage ... something 5.1 GXManageRealExp 5.2 GXManageExperiment 5.3 GXManageSamples 5.4 ImAnnoCluspackDisplay

General behaviour

the SelectFrom_listOfSomething or SelectMultipleFrom_listOfSomething asks the user to select one or more lines from ... Something.

In most of all cases the first line is '0 all concerned Something'. This means that in the processes it will concern no or all Something depeding on the context.

For example if we select '0 all concerned RealExp' in GXManageExperiment it means that the RealExp are simply not tested to determine which Experiment is to address.

General purpose tools

PasteToHtmlTable

PipeWorks create very often HtmlTable to display their results. It is a simple table with lines and columns. You can check any columns to redisplay it, and you can run the DoOnList on it.

• To get an HtmlTable from a text you prviously copy intp the clipboard, run the PipeWork 'PasteToHtmlTable', paste into the text area and press Evaluate.
• Lines have to be separated with newlines, words in a line have to be separated with tabs or space (please don't mix, I'm not shure it works well)
• If you want to give a name to your columns, add a first line with all keys as from example

 #KeysToUse:GeneName AccessNumber Length Sequence

GO PipeWork Reference Manual

• Actually we manage GO, Genes and Pfam
• You can get one type from an other. If you start from GO you can specify Down (or a positiv n) Up (or a negative n) or Here (0)
• You can store the result in a Store. For that change the 'GoStore*' to GoStoreMyBeautifulName
• You can recall these store with the select (it displays all stores starting with GoStore* (if you didn't change it)).

Go

The Go PipeWork

1. select within the 'From Go Pfam or Gene' (ie gene)
2. Enter the 'From list' (ie ion metal binding)
3. Select 'What to display' (ie GENEsymbol,fullname)
4. Enter the Level (ie Down to include all children, Up to include parents, Here or enter a number -2 Up, 0 Here, (+n skips 0))
5. Evaluate

You can also store the result, for that enter a name and click on the button from the line 'Click to store the result' To recall a previously stored result 'Select to recall it' and press Evaluate. I'm not sure it works well if you mix GOs and GENEs etc. So it should be better to enter a non existing Go for example XXXX.

GX PipeWork Reference Manual

GXRatio

Enter a Genelist or keep empty, select several RatioTypes or RealExpCondition or RealExpReference or several AnalysisSoftwares and press Evaluate. Then you get the ratio values which verify all these conditions.

• If you want all ratios of a genelist select '0 all concerned Ratiotype', 'O all concerned RealExpCon', etc.
• If you want the genes (probesets) for a given list of RatioTypes (or REalExpCon, etc) select your favorite RatioTypes (or REalExpCon, etc) and keep the genelist empty.

You can also choose the ratio characteritics interval (Minimum, Maximum). If Minimum is greater the Maximum we select the outer parts of the interval.

GXSamples

This PipeWork shows nicely all information concerning Samples.

You can select Samples directly within the list of available samples or through Experiments, RealExps and/or Arraytype

=GxManage ... something

All available GXManageXXX mainly allow to update or create new records in GxDb (you can also use the Show)

For a New, fill in all fields concerning name, description, ... and select the entities to which the foreign keys will point. (some fields are optional but there is no easy way to determine which one). ANd choos '0 all concerned XXX' For a Update leave blank the key you wan't update.

A good way to proceed is to

1. preselect the Enter, Select which will be mainly constant for what you are doing,
2. save the GXManageXXX as GXManageXXXTempo
3. do your New, Update, Clone
4. delete GXManageXXXTempo

GXManageRealExp

• GXManageRealExp allows to show, update, clone or create a new RealExp in GxDb
• You need to fill in all textual fields. Seelect the Arraytype, Sample, Experiment and evaluate

GXManageExperiment

• GXManageExperiment allows to show, update, clone or create a new Experiment in GxDb
• You need to fill in all textual fields. You can select several RealExp ... or do it later with GXManageRealExp.

GXManageSamples

A sample is defined by a Tissue, an Individual (defined by an Organism and a Genotype), a Treatment (with Treatmenttype).

All these entities can be shown, updated and created with this PipeWork

• GXManageSample allows to show, update or create a new Sample in GxDb
• GXManageSample allows to show, update or create a new Tissue in GxDb
• GXManageSample allows to show, update or create a new Individual in GxDb
• GXManageSample allows to show, update or create a new Organism in GxDb
• GXManageSample allows to show, update or create a new Genotype in GxDb
• GXManageSample allows to show, update or create a new Treatment in GxDb
• GXManageSample allows to show, update or create a new Treatmenttype in GxD

To run one of these Managing tool, select, update or create any missing entities, fill in the textual fields and evaluate the whole PipeWork or run separately it by clicking on the corresponding PWI button.

ImAnnoCluspackDisplay

This PipeWork allows to display the content of Cluspack data.

1. Select your cadre and organ (1 for eye, 2 for teeth, 3 for ear, 4 for eyefundus)
2. Select the Cluspack you want to dispaly and
3. Press 'Evaluate and keep your entries'