Merge pull request #43 from TheJacksonLaboratory/task/add-web-app-documentation

Adding web application specific documentation

Author: bergsalex

docs/assets/GeneWeaverquickstart2018.pdf

@@ -4,11 +4,27 @@ and concise introduction to the Geneweaver ecosystem. No matter who you are, thi
 section will help you quickly get up and running with basic features and functionalities
 in Geneweaver.
 
+## Quick Start
+-   The **[Quick Start Guide](../assets/GeneWeaverquickstart2018.pdf){:download="GeneWeaverQuickStart.pdf"}** is designed to help get new users up and running 
+quickly with a basic two page GeneWeaver Guide.
+-   The **[GeneWeaver Tutorial](../assets/gw-tutorial.pptx){:download="GeneWeaverTutorial.pptx"}** provides a guided tutorial exercise to get you 
+familiar with using and interpreting basic GeneWeaver analyses and tools through applied
+examples. The exercise is suitable for use in demonstrations, workshops and courses.
+
+* For more details on **how to get started** by searching for some specific genes of
+  interest and analyzing them, read the **[General Search](#general-search)** section.
+
+- To learn more about how to work with other researchers and their data within
+  GeneWeaver check out **[Users and Groups](#users-and-groups)**.
+- **[GeneWeaver Movie](https://www.youtube.com/watch?v=6mggK6tsEBo)** provides video
+  clips featuring examples of the use of GeneWeaver tools.
+- **[FAQ](#faq)**
+
 For more in-depth information about the concepts presented in this section, please see
 the [Concepts](../concepts/index.md) section and the [Reference](../reference/index.md)
 section.
 
-## Quick Start
+## Contextual Quick Start
 If you're already familiar with Geneweaver, and just need to find content specific to
 your use-case, you can use the following links to jump to the appropriate documentation.
 If you find that you need more information, head back to this website and keep reading!

docs/assets/gw-tutorial.pptx

@@ -36,142 +36,3 @@ Curation Tiers
 
 !!! tip
 	GeneSet tiers also have a non-curation meaning, which can be referenced on the [GeneSet Tiers](../geneset-tiers.md) page.
-
-# **General Definitions**
-
-**Gene Set Name**: A brief title for the gene set, approximately sentence length, that
-should provide a clear and concise description of the contents of a gene set
-interpretable to most users of GeneWeaver, but with sufficient detail to satisfy a
-domain expert. This is the major gene set name that is displayed in all search results,
-project directory and table views of analysis results. Standards for specific gene set
-types are given in the following section.
-
-**Gene Set Figure Label**: A brief 23 character abbreviation to facilitate recognition
-of the gene set in a graph or other display.
-
-**Gene Set Description**: A detailed description of the gene set, including rules for
-its construction, experimental methods and analyses used to generate data, anatomical
-terms, and traceable references to source data including accession information and date.
-Abbreviations should be avoided.
-
-**Ontology Annotations**: Relevant terms from Disease Ontology, Mammalian Ontology and
-other OBO ontologies supplied by curators or identified through the application of the
-NCBO Annotator to textual descriptions including publication abstracts.
-
-**Publication Information**:   PubMed ID, title, authors, publication information and
-full-text of the abstract.
-
-# **Standards for Common Gene Set Types**
-
-### Type of Data: Differential Expression Profiling
-
-**Gene Set Name**: Genes \[upregulated/downregulated/differentially expressed\] in
-\[tissue\] \[comparison\]. _**Example**_: Genes differentially expressed in striatum of
-C57Bl/6J compared to C57Bl/6C.
-Note: spell out anatomical terms as nouns, e.g. striatum, not striatal. Include complete
-strain names, e.g. C57BL/6J not B6.
-
-**Gene Set Figure Label**: B6JvsB6CStriatum
-
-**Gene Set Description**: Indicate which samples were compared. What experimental
-manipulations or tissue differences are being examined? Indicate statistical
-methodology, significance thresholds and which changes are reported here. Indicate if
-uploaded p-value, q-value, effect size or fold change and fold change reference.
-_**Example**_: Striatum gene expression differences between naive C57BL/6J and C57BL/6C
-substrains corresponding to a 5% FDR. A small number of genes are highly differentially
-expressed between B6 substrains, C57BL/6J (high alcohol consumption preference) and
-C57BL/6C (low alcohol consumption preference). Fold expression change are relative to
-B6/J.
-
-**Gene Set Contents**: Gene identifier and statistical score for differential
-expression, e.g. p-value, q-value, correlation coefficient, binary score, effect size or
-fold change.
-
-### Type of Data: Published QTL Candidate Gene List
-
-**Gene Set Name**: Description (name, Published QT Chr \# MGI:\#). _**Example**_:
-cocaine related behavior 10 (Cocrb10, Published QTL Chr \#)
-
-**Gene Set Figure Label**: (QTL-name-Organism-Chr \#). _**Example**_:
-QTL-Cocrb10-Mouse-Chr 9
-
-**Gene Set Description**: QTL Name Definition, candidate gene selection method (e.g. 1.5
-LOD drop; inter-marker interval). Exact description of phenotype. Strains used for
-mapping should be included. _**Example**_:                     Rats were subjected to a
-forced swim test (FST) procedure in which they are placed in water for 5 min, and their
-behavior was scored every 5 sec as immobility, climbing, or swimming. Data were analyzed
-for each activity with consideration given to their non-independence. p-value:0.0002,
-Variance: 3.6, Peak Marker: D5Rat40 (BLAT 16538053) Spans 1-41538053. This interval was
-obtained by using a fixed interval width of 25 Mbp around the peak marker. Strains were
-WKY/NHsd and F344/NHsd. Also defined as Imm3.
-
-**Gene Set Contents**: Gene identifier and binary score.
-
-### Type of Data: Co-Expression to Phenotype
-
-**Gene Set Name**: Describe tissue and phenotype correlated. _**Example**_: Cerebellum
-gene expression correlates of acetic acid writhing behavior in BXD recombinant inbred
-mice.
-
-**Gene Set Figure Label**: Co-expression writhing
-
-**Gene Set Description**: Indicate what the comparison was that was made and any
-statistical cut-offs that were used. _**Example**_: Cerebellum gene co-expression with
-acetic acid writhing in BXD RI mice. Gene expression data was obtained from
-genenetwork.org SJUT Cerebellum mRNA M430 (Mar05) RMA data set. Behavioral phenotype
-data was collected by RMQ and consisted of the number of writhes in response to 0.6%
-acetic acid i.p.
-
-**Gene Set Contents**: Gene identifier and statistical score for co-expression. e.g.
-R-squared, p-value, q-value, binary threshold.
-
-### Type of Data: Reference Ontology
-
-**Gene Set Name**: Term \# and name. _**Example**_: MP:XXXXXXX Abnormal.
-
-**Gene Set Figure Label**: Term \#. _**Example**_: Term \#
-
-**Gene Set Description**: Term Definition. _**Example**_: “Increase in the dose or
-concentration of a foreign compound required to induce a specific level of
-response” [www.informatics.jax.org](http://www.informatics.jax.org), 2010-12-01
-
-**Gene Set Contents**: All gene sets include genes, mutant alleles or gene products
-annotated to an ontology term by a professional curator. Each gene directly annotated to
-the term is given a score of 1, each gene connected to a term through annotations to its
-higher order parents is given a score of 2. To use only direct annotations in an
-analysis assign a threshold of < 2 to each Gene Set.
-
-### Type of Data: Co-Expression Clusters
-
-**Gene Set Name**: Co-Expression clusters. _**Example**_: Co-expression cluster of
-nicotine Dependence genes significantly expressed in the adolescent PFC, VS and
-Hippocampus.
-
-**Gene Set Figure Label**: Abbreviated description. _**Example**_: Adolesc Rat Nic
-Dependence
-
-**Gene Set Description**: Indicate what samples were compared and what was clustered.
-_**Example**_: Studies analyzing brain samples from female rats that had been injected
-with nicotine at four different ages show that nicotine exerts the greatest influence
-during adolescence. Using DNA microarrays, gene expression correlates were obtained from
-the prefrontal cortex (PFC), ventral striatum (VS), and hippocampus. Principal cluster
-analysis was then used to identify 76 genes that changed significantly in at least one
-of these three brain regions during the experiment.
-
-**Gene Set Contents**: Gene identifier and statistical score for cluster analysis or
-binary threshold.
-
-#### Type of Data: Genome Wide Association Study
-
-**Gene Set Name**: GWAS of ... _**Example**_: GWAS of Alcohol and Nicotine Dependence in
-Australian DNA-Pools.
-
-**Gene Set Figure Label**: Abbreviated description. _**Example**_: GWAS Alcohol Nicotine
-
-**Gene Set Description**: List of positional candidate genes after correcting for
-multiple testing and controlling the false discovery rate from genome wide association
-study. Represents genes associated with a linked cytological region or genes ‘near’ an
-associated SNP. _**Example**_: Genome-wide association study identifies a locus at
-7p15.2 associated with endometriosis.
-
-**Gene Set Contents**: Gene identifier and binary threshold.

docs/getting-started/index.md

@@ -0,0 +1,23 @@
+# **General Definitions**
+
+**Gene Set Name**: A brief title for the gene set, approximately sentence length, that
+should provide a clear and concise description of the contents of a gene set
+interpretable to most users of GeneWeaver, but with sufficient detail to satisfy a
+domain expert. This is the major gene set name that is displayed in all search results,
+project directory and table views of analysis results. Standards for specific gene set
+types are given in the following section.
+
+**Gene Set Figure Label**: A brief 23 character abbreviation to facilitate recognition
+of the gene set in a graph or other display.
+
+**Gene Set Description**: A detailed description of the gene set, including rules for
+its construction, experimental methods and analyses used to generate data, anatomical
+terms, and traceable references to source data including accession information and date.
+Abbreviations should be avoided.
+
+**Ontology Annotations**: Relevant terms from Disease Ontology, Mammalian Ontology and
+other OBO ontologies supplied by curators or identified through the application of the
+NCBO Annotator to textual descriptions including publication abstracts.
+
+**Publication Information**:   PubMed ID, title, authors, publication information and
+full-text of the abstract.

docs/reference/curation/curation-standards.md

@@ -0,0 +1,114 @@
+# **Standards for Common GeneSet Types**
+
+### Type of Data: Differential Expression Profiling
+
+**Gene Set Name**: Genes \[upregulated/downregulated/differentially expressed\] in
+\[tissue\] \[comparison\]. _**Example**_: Genes differentially expressed in striatum of
+C57Bl/6J compared to C57Bl/6C.
+Note: spell out anatomical terms as nouns, e.g. striatum, not striatal. Include complete
+strain names, e.g. C57BL/6J not B6.
+
+**Gene Set Figure Label**: B6JvsB6CStriatum
+
+**Gene Set Description**: Indicate which samples were compared. What experimental
+manipulations or tissue differences are being examined? Indicate statistical
+methodology, significance thresholds and which changes are reported here. Indicate if
+uploaded p-value, q-value, effect size or fold change and fold change reference.
+_**Example**_: Striatum gene expression differences between naive C57BL/6J and C57BL/6C
+substrains corresponding to a 5% FDR. A small number of genes are highly differentially
+expressed between B6 substrains, C57BL/6J (high alcohol consumption preference) and
+C57BL/6C (low alcohol consumption preference). Fold expression change are relative to
+B6/J.
+
+**Gene Set Contents**: Gene identifier and statistical score for differential
+expression, e.g. p-value, q-value, correlation coefficient, binary score, effect size or
+fold change.
+
+### Type of Data: Published QTL Candidate Gene List
+
+**Gene Set Name**: Description (name, Published QT Chr \# MGI:\#). _**Example**_:
+cocaine related behavior 10 (Cocrb10, Published QTL Chr \#)
+
+**Gene Set Figure Label**: (QTL-name-Organism-Chr \#). _**Example**_:
+QTL-Cocrb10-Mouse-Chr 9
+
+**Gene Set Description**: QTL Name Definition, candidate gene selection method (e.g. 1.5
+LOD drop; inter-marker interval). Exact description of phenotype. Strains used for
+mapping should be included. _**Example**_:                     Rats were subjected to a
+forced swim test (FST) procedure in which they are placed in water for 5 min, and their
+behavior was scored every 5 sec as immobility, climbing, or swimming. Data were analyzed
+for each activity with consideration given to their non-independence. p-value:0.0002,
+Variance: 3.6, Peak Marker: D5Rat40 (BLAT 16538053) Spans 1-41538053. This interval was
+obtained by using a fixed interval width of 25 Mbp around the peak marker. Strains were
+WKY/NHsd and F344/NHsd. Also defined as Imm3.
+
+**Gene Set Contents**: Gene identifier and binary score.
+
+### Type of Data: Co-Expression to Phenotype
+
+**Gene Set Name**: Describe tissue and phenotype correlated. _**Example**_: Cerebellum
+gene expression correlates of acetic acid writhing behavior in BXD recombinant inbred
+mice.
+
+**Gene Set Figure Label**: Co-expression writhing
+
+**Gene Set Description**: Indicate what the comparison was that was made and any
+statistical cut-offs that were used. _**Example**_: Cerebellum gene co-expression with
+acetic acid writhing in BXD RI mice. Gene expression data was obtained from
+genenetwork.org SJUT Cerebellum mRNA M430 (Mar05) RMA data set. Behavioral phenotype
+data was collected by RMQ and consisted of the number of writhes in response to 0.6%
+acetic acid i.p.
+
+**Gene Set Contents**: Gene identifier and statistical score for co-expression. e.g.
+R-squared, p-value, q-value, binary threshold.
+
+### Type of Data: Reference Ontology
+
+**Gene Set Name**: Term \# and name. _**Example**_: MP:XXXXXXX Abnormal.
+
+**Gene Set Figure Label**: Term \#. _**Example**_: Term \#
+
+**Gene Set Description**: Term Definition. _**Example**_: “Increase in the dose or
+concentration of a foreign compound required to induce a specific level of
+response” [www.informatics.jax.org](http://www.informatics.jax.org), 2010-12-01
+
+**Gene Set Contents**: All gene sets include genes, mutant alleles or gene products
+annotated to an ontology term by a professional curator. Each gene directly annotated to
+the term is given a score of 1, each gene connected to a term through annotations to its
+higher order parents is given a score of 2. To use only direct annotations in an
+analysis assign a threshold of < 2 to each Gene Set.
+
+### Type of Data: Co-Expression Clusters
+
+**Gene Set Name**: Co-Expression clusters. _**Example**_: Co-expression cluster of
+nicotine Dependence genes significantly expressed in the adolescent PFC, VS and
+Hippocampus.
+
+**Gene Set Figure Label**: Abbreviated description. _**Example**_: Adolesc Rat Nic
+Dependence
+
+**Gene Set Description**: Indicate what samples were compared and what was clustered.
+_**Example**_: Studies analyzing brain samples from female rats that had been injected
+with nicotine at four different ages show that nicotine exerts the greatest influence
+during adolescence. Using DNA microarrays, gene expression correlates were obtained from
+the prefrontal cortex (PFC), ventral striatum (VS), and hippocampus. Principal cluster
+analysis was then used to identify 76 genes that changed significantly in at least one
+of these three brain regions during the experiment.
+
+**Gene Set Contents**: Gene identifier and statistical score for cluster analysis or
+binary threshold.
+
+#### Type of Data: Genome Wide Association Study
+
+**Gene Set Name**: GWAS of ... _**Example**_: GWAS of Alcohol and Nicotine Dependence in
+Australian DNA-Pools.
+
+**Gene Set Figure Label**: Abbreviated description. _**Example**_: GWAS Alcohol Nicotine
+
+**Gene Set Description**: List of positional candidate genes after correcting for
+multiple testing and controlling the false discovery rate from genome wide association
+study. Represents genes associated with a linked cytological region or genes ‘near’ an
+associated SNP. _**Example**_: Genome-wide association study identifies a locus at
+7p15.2 associated with endometriosis.
+
+**Gene Set Contents**: Gene identifier and binary threshold.

docs/reference/curation/general-definitions.md

@@ -0,0 +1,28 @@
+# Batch Gene Set Upload
+
+If you have many gene sets to upload, for example, the results of a clustering analysis,
+use the bulk upload form. An example of a bulk upload file is provided. Contact the
+GeneWeaver team for assistance with very large batch submissions and integration of
+large scale data resources.
+
+On the navigation bar, under "Manage GeneSets" select "Upload Batch GeneSets".
+
+![](../assets/images/Batch-upload-page.png)
+
+This page requires that a group is selected to curate the genesets. A private group can
+be used if the data will not become public. To learn why curation is necessary and how
+to curate go [here](../../reference/curation/).
+
+A sample upload file that includes the formatting rules is displayed on the page and a
+sample file may also be opened by clicking on the "Sample File" link.
+
+When your file is prepared, click on "Batch Upload File" to select it. Then click on "
+Review GeneSet Upload" to start the upload process.
+
+When completec, review the results of the upload and add annotations.
+See [gene set details](../view-genesets/#geneset-details-pages). To use your new gene 
+set in analyses, you must add it to [projects](../projects/).
+
+
+
+

docs/reference/curation/geneset-type-standards.md

@@ -0,0 +1,27 @@
+**Notifications**
+=================
+Notifications are the mechanism GeneWeaver uses to send messages within the application.
+There is also an option to receive email for notifications, which can be controlled from
+the **[Account Settings](../users-and-groups/#accounts-page)** page.
+
+![](images/Image072.png)
+
+![](images/Image074.png)
+
+Regardless of whether a user has been configured to receive
+emails, they will always receive messages through the **Notifications** page. The fact
+that you have pending notifications will be noted in the menu bar by a red indicator
+over the envelope icon.
+
+![](images/Image076.png)
+
+The **Notifications** page itself is fairly straight forward listing the notifications
+that have not yet been seen in bold, and the rest of the notifications in normal font.
+There is a button at the bottom of the page that allows you to **Load More Notifications
+** so that you can get your full history of notifications.
+
+![](images/Image078.png)
+
+
+
+