added new issues: bulklmm, Pluto notebooks, geno file HSNIH Palmer

3 files changed, 67 insertions, 0 deletions

diff --git a/issues/add-bulklmm-feature.gmi b/issues/add-bulklmm-feature.gmi
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+## BulkLMM integration
+
+## Tags
+
+* assigned: pjotrp
+* type: feature
+* priority: high
+
+## Description
+
+Integrate BulkLMM in GeneNetwork. The first step is to test the command line interface to BulkLMM in GeneNetwork using the BulkLMMSysimage. 
+The BulkLMMSysimage files provides instructions for generating the BulkLMM.jl sysimage,along with the code for the command-line functions.
+
+=> https://github.com/senresearch/BulkLMMSysimage	BulkLMMSysimage files
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diff --git a/issues/add-pluto-notebooks.gmi b/issues/add-pluto-notebooks.gmi
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+## Add Pluto Notebooks
+
+## Tags
+
+* assigned: pjotrp
+* type: feature
+* priority: high
+
+## Description
+
+Host Pluto Notebooks in GeneNetwork. As a proof of concept, we host:
+
+=> https://notebooks.one/	notebooks.one
+
+We used the package PlutoSliderServer.jl:
+
+=> https://github.com/JuliaPluto/PlutoSliderServer.jl	PlutoSliderServer.jl
+
+See also our deployment repo for notebooks.one:
+
+=> https://github.com/GregFa/visuals/tree/testing
+
+Considering its capabilities, PlutoSliderServer.jl could potentially serve as a viable solution for hosting Pluto Notebooks on GeneNetwork.
diff --git a/issues/fix-genotype-filename-HSNIH-Palmer.gmi b/issues/fix-genotype-filename-HSNIH-Palmer.gmi
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+## Fix genotype filename HSNIH-Palmer
+
+## Tags
+
+* assigned: pjotrp
+* type: bug fix
+* priority: high
+
+## Description
+
+
+When using the Rest API to get the groups for "rat", it mentions the group HSNIH-Palmer.
+But the REST API to obtain the geno file(http://gn2.genenetwork.org/api/v_pre1/gentotypes/HSNIH-Palmer.geno) failed.
+The file of HSNIF-Palmer has actually a different name from what is expected; we have to use "HSNIH-Palmer_true" instead.
+On GeneNetwork website, the following query does not return results from the search.
+
+Dataset try to access: HSNIH-Palmer
+
+Issues with genotyped data:
+Used this query:
+
+Species: Rat
+
+Group: NIH Heterogeneous Stock (Palmer)
+
+Type: DNA Markers and SNPs
+
+Dataset: HSNIH-Palmer Genotypes
+
+Get Any: *