sulab / biogps_core Goto Github PK

For example, data chart plugin executes this call: http://biogps.org/dataset/search/?&page=1&reporters=NM_001798.3,NM_052827.2,1792_g_at,1833_at,204252_at,211803_at,211804_s_at,441&q=fat

each matching data set returns id, name, and factors. In addition, return all metadata that is shown in dataset library search (e.g., owner, species, tags, description).

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/11
• Originally reported by: Andrew Su
• Originally created at: 2013-01-15T22:03:56.413

In chrome, the outer-most vertical scrollbar does not appear to work. See the attached screenshot. Works fine in IE9 and Firefox.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/14
• Originally reported by: Andrew Su
• Originally created at: 2013-01-17T06:27:38.494

From a mouse dataset (e.g., "GeneAtlas MOE430, gcrma" http://biogps.org/dataset/4/), the link for "View Dataset" goes to the human version of CDK2 (http://biogps.org/#goto=genereport&id=1017&show_dataset=4). Of course, the data chart viewer reports that this gene has no data in this data set. The link instead should go to a species-appropriate gene report (e.g., http://biogps.org/#goto=genereport&id=12566&show_dataset=4).

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/27
• Originally reported by: Andrew Su
• Originally created at: 2013-03-07T22:22:48.798

I think many plugin owners create a plugin (or have one transferred to them) and then promptly forget about it. We should create a monthly report that goes to each plugin creator describing all usage metrics we can find: # layouts, # users, # impressions, etc.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/48
• Originally reported by: Andrew Su
• Originally created at: 2014-11-08T01:21:01.299

Award users with various "badges" for qualified user actions:

• register a plugin
• complete profile
• report a broken plugin

etc.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/21
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T22:43:38.948

Currently flagging plugins is limited to users who are logged in. Since the many of our users are "anonymous", better to allow anyone to flag.

Right now, I'm discovering by chance many plugins whose URL Templates need to be updated. I'd like to enable the community to better notify us when plugins are broken.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/2
• Originally reported by: Su Lab
• Originally created at: 2012-04-30T19:42:23.579

We need to build a tool to load all GEO GDS datasets (GDS datasets contain curated metadata) It should support incremental update.

Useful resources:

• http://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html
• http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/37
• Originally reported by: Chunlei Wu
• Originally created at: 2013-11-20T00:39:55.422

The plugin registration form contains a "Summary" field that is capped at 140 characters. Right now the text input box only allows 140 characters to be entered at any one time. For example, if a 160 character string is pasted into the box, it is truncated at 140 characters.

A better behavior would be to mirror the twitter interface. Any length character can be pasted in, but the "submit" button is greyed out when the string is too long. In addition, the character counter shows a negative number. See the attached screenshot from tweetdeck...

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/35
• Originally reported by: Andrew Su
• Originally created at: 2013-10-24T02:19:57.894

Currently, sitemap generation (/sitemap.xml) relies on "biogps.www.models.BiogpsRootnode" model (in src/biogps/www/sitemap.py). Available gene ids are manually populated into BiogpsRootnode model from mygene.info.

To make sure sitemap is always up-to-date for what "mygene.info" provides, we should re-write the mechanism to make query directly on mygene.info to get the up-to-date gene id list. And even better, we can build a caching mechanism to cache the gene id list locally or on DB, that way, we can avoid the repeated heavy queries on mygene.info.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/24
• Originally reported by: Chunlei Wu
• Originally created at: 2013-02-25T23:18:30.204

We should make a smoother interface for the flow of "Query-Result-GeneReport", which is based on a tab interface currently.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/17
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T21:50:03.052

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/41
• Originally reported by: Chunlei Wu
• Originally created at: 2013-11-25T23:24:26.780

In Google Chrome, several javascript errors like this one:

#!

Unsafe JavaScript attempt to access frame with URL http://en.wikipedia.org/wiki/Cyclin-dependent_kinase_2 from frame with URL http://biogps.org/#goto=genereport&id=1017. Domains, protocols and ports must match.

occurs. Firefox and IE do not have these errors.

The error can been traced down to "miframe-debug.js" javascript file (ManagedIframe under development mode.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/23
• Originally reported by: Chunlei Wu
• Originally created at: 2013-02-23T07:08:20.634

We have built a MongoDB-based gene list backend, we should integrate it into BioGPS. Besides the management of users' own gene lists, A major feature is to allow users to query a gene list for functional enrichment.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/18
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T21:54:36.945

Default (and current) sort-by is by popularity. Add sort-by date. For dataset library, add sort-by number of samples

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/4
• Originally reported by: Andrew Su
• Originally created at: 2012-12-14T19:39:17.506

http://orcid.org

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/44
• Originally reported by: Chunlei Wu
• Originally created at: 2014-05-03T00:13:45.627

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/43
• Originally reported by: Chunlei Wu
• Originally created at: 2014-04-18T00:58:26.896

e.g., http://biogps.org/dataset/search/?&page=1&reporters=NM_001798.3,NM_052827.2,1792_g_at,1833_at,204252_at,211803_at,211804_s_at,477&q=cancer

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/12
• Originally reported by: Andrew Su
• Originally created at: 2013-01-15T22:21:38.965

So far I've only seen this for plugins that use {{MGI}} (e.g., http://biogps.org/plugin/120/international-mouse-strain-resource-jackson-laboratory/, http://biogps.org/plugin/30/mouse-genome-informatics-mgi/). I haven't extensively tested this for other keywords.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/1
• Originally reported by: Su Lab
• Originally created at: 2012-04-30T19:39:49.198

Display users' last "N" activities (such as gene query, plugin, layout, gene list usages).

Potentially, can be other users' activity from friends circle.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/22
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T22:46:17.914

A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing

http://www.cell.com/abstract/S0092-8674(07)00604-6

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/46
• Originally reported by: Chunlei Wu
• Originally created at: 2014-11-06T18:57:07.311

Currently plugin popularity is based on usage in a gene report layout (i.e. how many layouts add this plugin). Another useful metrics is how many times this plugin is actually be viewed in gene report page.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/15
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T21:42:21.035

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/10
• Originally reported by: Andrew Su
• Originally created at: 2013-01-15T21:58:07.529

number of samples, upload date, rating

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/13
• Originally reported by: Andrew Su
• Originally created at: 2013-01-15T22:22:52.163

Currently, GEO dataset queries are against "summary", "sample descriptions" and other metadata. Each GEO dataset should have an associated publication, it would be nice to index its PubMed abstract for dataset queries as well (or, run NCBO annotator to extract the relevant "concepts" only).

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/26
• Originally reported by: Chunlei Wu
• Originally created at: 2013-03-01T02:44:47.158

Currently an email is sent to administrators when a new plugin is created. We should embed a link in that email to "tweet this" from the BioGPS twitter account. Probably should only be for public plugins...

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/30
• Originally reported by: Andrew Su
• Originally created at: 2013-06-06T02:32:34.757

The plugin registration form has a field for "Full description", but that currently is text-only. Would like to make that markdown-capable.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/7
• Originally reported by: Andrew Su
• Originally created at: 2013-01-08T23:50:23.503

When loading GEO datasets, the "summary" field should be imported into the metadata. There was a bug importing the summary for GSE18842. The summary right now only reads "PURPOSE", presumably because it was truncated at the first newline in the GEO entry (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18842). If this diagnosis is correct, then the GEO data importer should be fixed to import the entire summary field.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/36
• Originally reported by: Andrew Su
• Originally created at: 2013-11-16T02:00:11.485

Currently, when browsing the dataset and plugin libraries, the search box prepopulates with a "in:plugin" or "in:dataset" filter. To make this filter even more intuitive, change the styling so the filter shows up as a button (with an "X" to remove). See the attached screenshot as an example (from https://google-developers.appspot.com/chart/interactive/docs/gallery/linechart).

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/6
• Originally reported by: Andrew Su
• Originally created at: 2012-12-26T20:32:01.576

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203610/

The microRNA body map: dissecting microRNA function through integrative genomics

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/45
• Originally reported by: Chunlei Wu
• Originally created at: 2014-11-06T18:56:26.414

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/28
• Originally reported by: Chunlei Wu
• Originally created at: 2013-04-06T02:39:17.292

When searching using the "Quick add" feature, the matching plugins should be sorted by plugin popularity (as measured by layout usage). That feature is apparently currently broken (see screenshot). Same for searching directly within the plugin library (e.g., http://biogps.org/search/?q=in%3Aplugin+gene+expression)...

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/9
• Originally reported by: Andrew Su
• Originally created at: 2013-01-15T02:10:54.725

To refactor current genereport page to a standalone page without EXT-JS based tab-panel interface.

• a standalone page with /gene/ URL pattern
• fits the overall themes used in plugin/dataset pages.
• thin header with search bar
• gene list from search result rendered in a left-side slide-out box.
  something like this: http://tympanus.net/codrops/2013/07/30/google-nexus-website-menu/

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/40
• Originally reported by: Chunlei Wu
• Originally created at: 2013-11-25T23:20:56.590

This can be a good model to follow.

An example here: https://github.com/celery/celery/issues?labels=&page=1&state=open

(also note how the URL changes when selecting facets.)

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/39
• Originally reported by: Chunlei Wu
• Originally created at: 2013-11-23T16:30:52.414

http://www.riken.jp/en/pr/press/2014/20140327_1/

download here: http://fantom.gsc.riken.jp/5/data/

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/42
• Originally reported by: Chunlei Wu
• Originally created at: 2014-03-27T19:43:28.426

Download link: http://www.broadinstitute.org/ccle/data/browseData?conversationPropagation=begin

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/38
• Originally reported by: Chunlei Wu
• Originally created at: 2013-11-20T00:49:09.549

http://www.gtexportal.org/

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/49
• Originally reported by: Chunlei Wu
• Originally created at: 2014-12-04T19:24:19.657

Noticeable performance drop for BioGPS website in some regions (e.g. EU, maybe Asia).

"Latency Based Routing (LBR) for Amazon Route 53" mentioned at the bottom of this thread might be a solution:

https://forums.aws.amazon.com/thread.jspa?threadID=56037&start=25&tstart=0

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/16
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T21:46:45.828

After a user creates a plugin, they see a modal window to "Go to plugin". In addition, there should be a "tweet this" button that allows them to tweet from their own twitter account.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/31
• Originally reported by: Andrew Su
• Originally created at: 2013-06-06T02:34:44.962

right now, it takes a r cutoff value, returns all hits with higher r values.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/29
• Originally reported by: Chunlei Wu
• Originally created at: 2013-04-06T02:41:24.554

right now, deleting a plugin from a layout causes a dialog box to come up asking 'Are you sure that you want to remove this plugin "..." from your layout?'. Instead, let's have the plugin be removed immediately and have an "undo" link appear in the header for 10 seconds, similar to how Gmail does it...

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/5
• Originally reported by: Andrew Su
• Originally created at: 2012-12-21T06:29:34.555

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2706/ from
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3080.html

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/50
• Originally reported by: Andrew Su
• Originally created at: 2014-12-10T06:21:58.512

From Tom Freeman: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49910

Still getting more info from him regarding ordering, naming, coloring...

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/34
• Originally reported by: Andrew Su
• Originally created at: 2013-08-22T19:25:37.351

The front page of BioGPS displays the most recent blog posts tagged with "biogps" from the Su Lab Blog. However, special characters are not rendered correctly. For example, apostrophes are rendered as HTML-escaped ’ See attached screenshot...

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/8
• Originally reported by: Andrew Su
• Originally created at: 2013-01-08T23:54:42.942

This is to allow a new type of plugins, which accept a list of gene ids as the input. While the current plugins typically accept a single gene at a time.

Typical use cases, such as gene enrichment analysis, pathway display, expression profile queries, etc.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/19
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T21:57:08.370

As a work around, this query can boost the exact match with gene symbol (e.g. "cdk2" as the query term):

symbol:cdk2 OR symbol:cdk2* OR name:cdk2* OR summary:cdk2*

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/3
• Originally reported by: Chunlei Wu
• Originally created at: 2012-06-20T01:50:43.437

CSV file attached -- data processed by Katie; raw counts shown. More info at the GEO record: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30611

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/33
• Originally reported by: Andrew Su
• Originally created at: 2013-08-22T19:23:04.908

To return recommended plugins based on user's plugin usage.

A placeholder for now. Need more details provided.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/20
• Originally reported by: Chunlei Wu
• Originally created at: 2013-01-28T22:39:35.175

For example, see the chart here: http://biogps.org/dataset/6/chart/1570051_at/ (also attached as screenshot). Because there are so many samples in this data set, the labels are illegible.

This chart is generated by the Google Chart API. As one possible solution, have the requested image height be proportional to the number of samples in the data set.

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/25
• Originally reported by: Andrew Su
• Originally created at: 2013-02-26T02:44:55.130

Despite the fact that we have a system for users to report broken plugins, it's apparent that most people don't. (e.g., Human Protein Atlas is one of our most used plugins, and that one didn't get reported...) So I think we need to build some sort of system so that we can review plugins in a fully- or semi-automatic method. It doesn't have to be perfect, but we need to do something...

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/47
• Originally reported by: Andrew Su
• Originally created at: 2014-11-08T00:59:19.652

For sites that set "X-Frame-Options" to "same-origin", content does not render in BioGPS plugins. Create a "render_as_link" option that displays a link to the content instead of the content itself.

Examples: All google-based plugins, "Mouse Resources Portal (Sanger)" plugin

• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/32
• Originally reported by: Andrew Su
• Originally created at: 2013-07-19T00:40:07.289