<commit_before># Web Apollo Testing Script

093014

<NAME>

Note: The following steps are meant for testing purposes only, not for training manual annotators.

## Web Apollo General Information
- The Web Apollo website:
http://GenomeArchitect.org
- The article describing Web Apollo can be found at:  
http://genomebiology.com/2013/14/8/R93/abstract
- The public Web Apollo honey bee (Apis mellifera) demonstration site is available at: 
http://genomearchitect.org/WebApolloDemo/
- You may find our user guide at:
http://genomearchitect.org/web_apollo_user_guide
- You may find a few slide presentations on the 'How Tos' of Web Apollo at:
http://www.slideshare.net/MonicaMunozTorres/
- Web Apollo at GMOD page: 
http://www.gmod.org/wiki/WebApollo 

If testing the Web Apollo demo, go to: http://genomearchitect.org/WebApolloDemo/ 
Login|Password : <PASSWORD>


## Testing a Web Apollo Instance

###Testing functions in the main window

1) Check display of tracks by "check" and "uncheck" clicks on list of evidence tracks. Display evidence available on other tracks. 

2) Drag and drop a gene onto the “User-created Annotations” (U-cA) area.

3) Test top-level menu options in the main window.

3.1) Test functions on each menu option:

-- Login: login/logout. 

-- File 

   /Open (Test that data can be loaded locally using URLs (File / Open / Remote URLs)).

   /Add Combination Track (see 10. below)

   /Add Sequence Search Track (perform search test)

-- Tools (see 3.2)

-- View: set and clear highlights, show plus/minus strands, resize quantitative tracks, color by CDS (also tested in 5).

3.2) From “Tools” menu, query genome with BLAT using a sequence: 

E.g: Housekeeping gene Calpain small subunit 1 CPNS1, CAPNS1, CAPN4, CAPNS (UniProt).

>sp|P04632|CPNS1_HUMAN Calpain small subunit 1 MFLVNSFLKGGGGGGGGGGGLGGGLGNVLGGLISGAGGGGGGGGGGGGGGGGGGGGTAMRILGGVISAISEAAAQYNPEPPPPRTHYSNIEANESEEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKRWQAIYKQFDTDRSGTICSSELPGAFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS

3.3) Clear highlight using the command from the 'View' menu.

4) Search for an indexed gene (e.g. in honey bee demo CSN2_DANRE (it's on Group1.37:152689..155265)) by typing the gene name on the search box. 

5) Zoom in (double click) to inspect last exon (5'-3') of the displayed gene and:

-- change intron/exon boundary (dragging)<commit_msg>Testing a web apollo instance<commit_after># Web Apollo Testing Script

093014

<NAME>

Note: The following steps are meant for testing purposes only, not for training manual annotators.

## Web Apollo General Information
- The Web Apollo website:
http://GenomeArchitect.org
- The article describing Web Apollo can be found at:  
http://genomebiology.com/2013/14/8/R93/abstract
- The public Web Apollo honey bee (Apis mellifera) demonstration site is available at: 
http://genomearchitect.org/WebApolloDemo/
- You may find our user guide at:
http://genomearchitect.org/web_apollo_user_guide
- You may find a few slide presentations on the 'How Tos' of Web Apollo at:
http://www.slideshare.net/MonicaMunozTorres/
- Web Apollo at GMOD page: 
http://www.gmod.org/wiki/WebApollo 

If testing the Web Apollo demo, go to: http://genomearchitect.org/WebApolloDemo/ 
Login|Password : <PASSWORD>


## Testing a Web Apollo Instance

###Testing functions in the main window

1) Check display of tracks by "check" and "uncheck" clicks on list of evidence tracks. Display evidence available on other tracks. 

2) Drag and drop a gene onto the “User-created Annotations” (U-cA) area.

3) Test top-level menu options in the main window.

3.1) Test functions on each menu option:

-- Login: login/logout. 

-- File 

   //Open (Test that data can be loaded locally using URLs (File / Open / Remote URLs)).

   /Add Combination Track (see 10. below)

   /Add Sequence Search Track (perform search test)

-- Tools (see 3.2)

-- View: set and clear highlights, show plus/minus strands, resize quantitative tracks, color by CDS (also tested in 5).

3.2) From “Tools” menu, query genome with BLAT using a sequence: 

E.g: Housekeeping gene Calpain small subunit 1 CPNS1, CAPNS1, CAPN4, CAPNS (UniProt).

>sp|P04632|CPNS1_HUMAN Calpain small subunit 1 MFLVNSFLKGGGGGGGGGGGLGGGLGNVLGGLISGAGGGGGGGGGGGGGGGGGGGGTAMRILGGVISAISEAAAQYNPEPPPPRTHYSNIEANESEEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKRWQAIYKQFDTDRSGTICSSELPGAFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS

3.3) Clear highlight using the command from the 'View' menu.

4) Search for an indexed gene (e.g. in honey bee demo CSN2_DANRE (it's on Group1.37:152689..155265)) by typing the gene name on the search box. 

5) Zoom in (double click) to inspect last exon (5'-3') of the displayed gene and:

-- change intron/exon boundary (dragging)
{'fraction_non_alphanumeric': 0.0781926965133072, 'fraction_numerical': 0.024757582009490405, 'mean_word_length': 4.509090909090909, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 4, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2846245', 'n_tokens_mistral': 1817, 'n_tokens_neox': 1596, 'n_words': 581}