Loading man/man_howto.md +1 −1 Original line number Diff line number Diff line Loading @@ -375,7 +375,7 @@ about the subject. This section just deals with the available annot commands. them when available and backs up the local modifications. How to is described in the last step of *HowTo install annot?* Some ontologies we had to defind our own, because no established ontology was available. We have defined ontologies for categories where no established ontology exists. For example: Dye, Health status, Provider, Sample entity, Verification profile and Yield fraction. Terms added to these ontologies can be transformed to "original" ontology terms: Loading man/man_tutorial.md +6 −6 Original line number Diff line number Diff line Loading @@ -262,12 +262,12 @@ The *third part* builds an acjson object. Acjson stands for *assay coordinate ja s_log='from the bricks' ) ``` As you can see, as annot wrote the template code, it was able to give, based on the setname meaning full `s_runid`, `s_runtype` and `s_log`. However there are some questions marks (`?`) in the code. This is because the wellplate layout has not yet been specified. You could for example specify a 384 wellplate (16x24) or a 96 wellplate (8x12) or petri dish (1x1) or a tube (1x1). We set `s_welllayout` to `1x1` because we will treatat all our wells with the same lapatinib concentration. Notably, in the template code, annot was able to specify `s_runid`, `s_runtype` and `s_log`. The question marks (`?`) in the code reflect that the wellplate layout, spot layout, concentration and reaction time has not yet been specified. You could for example specify a 384 wellplate (`16x24`) or a 96 wellplate (`8x12`) or petri dish (`1x1`) or a tube (`1x1`). We set `s_welllayout` to `1x1` because we will treat all our wells with the same lapatinib concentration. Annot can handle arrays with multiple spots per well. However, we will leave `ti_spotlayout` by the default which is `(1,)`, since lapatinib not is spotted to the array. Loading Loading
man/man_howto.md +1 −1 Original line number Diff line number Diff line Loading @@ -375,7 +375,7 @@ about the subject. This section just deals with the available annot commands. them when available and backs up the local modifications. How to is described in the last step of *HowTo install annot?* Some ontologies we had to defind our own, because no established ontology was available. We have defined ontologies for categories where no established ontology exists. For example: Dye, Health status, Provider, Sample entity, Verification profile and Yield fraction. Terms added to these ontologies can be transformed to "original" ontology terms: Loading
man/man_tutorial.md +6 −6 Original line number Diff line number Diff line Loading @@ -262,12 +262,12 @@ The *third part* builds an acjson object. Acjson stands for *assay coordinate ja s_log='from the bricks' ) ``` As you can see, as annot wrote the template code, it was able to give, based on the setname meaning full `s_runid`, `s_runtype` and `s_log`. However there are some questions marks (`?`) in the code. This is because the wellplate layout has not yet been specified. You could for example specify a 384 wellplate (16x24) or a 96 wellplate (8x12) or petri dish (1x1) or a tube (1x1). We set `s_welllayout` to `1x1` because we will treatat all our wells with the same lapatinib concentration. Notably, in the template code, annot was able to specify `s_runid`, `s_runtype` and `s_log`. The question marks (`?`) in the code reflect that the wellplate layout, spot layout, concentration and reaction time has not yet been specified. You could for example specify a 384 wellplate (`16x24`) or a 96 wellplate (`8x12`) or petri dish (`1x1`) or a tube (`1x1`). We set `s_welllayout` to `1x1` because we will treat all our wells with the same lapatinib concentration. Annot can handle arrays with multiple spots per well. However, we will leave `ti_spotlayout` by the default which is `(1,)`, since lapatinib not is spotted to the array. Loading
