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Analytics and help page
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| {% extends "base.html" %} {% block content %} | ||
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| <!-- Staring definition of site content --> | ||
| <section class="section"> | ||
| <div class="box"> | ||
| <section class="section"> | ||
| <div class='content'> | ||
| <h1 class="title" style="color: #00AFDC;">Help</h1> | ||
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| <h3 class="title" style="color: #00AFDC;">Tutorial</h3> | ||
| <p> | ||
| To get more familiar with the using MetaDome and all of it's functionality | ||
| we strongly advise to <a href="{{ url_for('web.dashboard') }}?tour=true"> | ||
| start the tour</a>. If you feel that any questions are not addressed in the | ||
| FAQ below, please <a href="{{ url_for('web.contact') }}">contact us</a>. | ||
| </p> | ||
|
|
||
| <h3 class="title" style="color: #00AFDC;">Privacy</h3> | ||
| <p> | ||
| This section outlines the ways in which the MetaDome website handles information about users. | ||
| This should not be read as a legal document, but as a description of how we handle information | ||
| that could be considered sensitive. | ||
| </p> | ||
| <div class="label">Sensitive data</div> | ||
| <p> | ||
| MetaDome does not save any data that a user may provide. The visualization | ||
| of MetaDome occurs client-side (in your local browser) and is not | ||
| accessible to us. This means we can not know which genes, transcripts, | ||
| domains, and positions you are interested in. | ||
| </p> | ||
|
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| <div class="label">Personalized tracking</div> | ||
| <p> | ||
| MetaDome makes use of <a href="http://www.google.com/analytics/" | ||
| target="_blank">Google analytics</a> (GA) to help us analyze how users | ||
| navigate the various site-pages. | ||
| GA uses a single-pixel "web bug" image, which is served from every | ||
| page, a javascript script that collects information about each request, | ||
| and cookies that maintain information about your usage of the site between | ||
| visits. You can read more about how GA works on the GA | ||
| <a href="http://www.google.com/analytics/" target="_blank">website</a>, | ||
| which includes a <a class="ext" href="http://code.google.com/apis/analytics/docs/concepts/gaConceptsOverview.html"> | ||
| detailed description</a> of how traffic is tracked and analysed. | ||
| <br><br> | ||
| We use the information generated by GA purely to assess the usefulness | ||
| and popularity of different features of the site. We have configured GA | ||
| to not provide the ability to track individual users' usage of the site. | ||
| However, GA does provides a high-level anonymized overview of the traffic that passes | ||
| through the site, including such information as the approximate geographical | ||
| location of users, how often and for how long they visited the site, etc. | ||
| <br><br> | ||
| We will never (and will not allow any third party to) use the | ||
| information by the GA to track or to collect any Personally | ||
| Identifiable Information of visitors to our site. | ||
| Neither will we will link, or seek to link, an IP address | ||
| with the identity of a computer user. | ||
| <br><br> | ||
| If you have any concerns about our use of Google analytics, please | ||
| feel free to <a href="{{ url_for('web.contact') }}">contact us</a>. | ||
| </p> | ||
|
|
||
| <h1 class="title" style="color: #00AFDC;">Frequently Asked Questions</h1> | ||
|
|
||
| <h3 class="title" style="color: #00AFDC;">General questions</h3> | ||
| <div class="box"> | ||
| <div class="label">What is MetaDome?</div> | ||
| <div class="box"> | ||
| MetaDome is a fast and easy-to-use web server that offers an easily | ||
| accessible and unique perspective that enables researchers and | ||
| clinicians to interpret variants of unknown significance via | ||
| 'meta-domains'; a concept that we have previously validated | ||
| (<a href="https://doi.org/10.1002/humu.23313" target="_blank"> | ||
| L. Wiel et al. Human Mutation, 2017 </a>) which makes use of protein | ||
| domain homology within the human genome to transfer genetic variant | ||
| information across homologous domains. MetaDome can visualize | ||
| meta-domain information and gene-wide profiles of genetic tolerance. | ||
| </div> | ||
|
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||
|
|
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| <div class="label">How can I use MetaDome?</div> | ||
| <div class="box"> | ||
| Analyses through MetaDome can be performed by querying a gene name | ||
| and desired transcript. The result is a visualization that a user | ||
| may interact with to highlight positions of their interest and | ||
| obtain more detailed information of those positions. This includes | ||
| regional tolerance to missense variation and the presence or absence | ||
| of variation at corresponding positions within homologous domains. | ||
| <br><br> | ||
| To get more familiar with the using MetaDome and all of it's functionality | ||
| we strongly advise to <a href="{{ url_for('web.dashboard') }}?tour=true"> | ||
| start the tour</a>. | ||
| </div> | ||
|
|
||
| <div class="label">Can I use my smartphone or tablet to access MetaDome?</div> | ||
| <div class="box"> | ||
| Although we recommend using a laptop/desktop with a compatible | ||
| browser for the best user experience, we designed the user interface | ||
| to be useable for mobile devices as well. If you encounter any problems or | ||
| see any possible improvements please | ||
| <a href="{{ url_for('web.contact') }}">contact us</a>. | ||
| </div> | ||
|
|
||
| <div class="label">What desktop browsers are compatible for MetaDome?</div> | ||
| <div class="box"> | ||
| <p> | ||
| The MetaDome web server is developed and extensively tested using | ||
| <a href="https://www.google.com/chrome/">Google Chrome</a> and | ||
| <a href="https://www.mozilla.org/en-US/firefox/new/">Firefox</a>. We | ||
| recommend using one of these browsers to access all functionality. | ||
| Here is a list of compatible and tested browsers: | ||
| </p> | ||
| <table class="table"> | ||
| <thead> | ||
| <tr> | ||
| <th><abbr title="OS">OS</abbr></th> | ||
| <th><abbr title="Version">Version</abbr></th> | ||
| <th><abbr title="Chrome">Chrome</abbr></th> | ||
| <th><abbr title="Firefox">Firefox</abbr></th> | ||
| <th><abbr title="Microsoft Edge">Microsoft Edge</abbr></th> | ||
| <th><abbr title="Microsoft IE">Microsoft IE</abbr></th> | ||
| <th><abbr title="Safari">Safari</abbr></th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| <tr> | ||
| <th>Linux</th> | ||
| <td>Ubuntu 16.04 and 18.04</td> | ||
| <td>70.0</td> | ||
| <td>63.0</td> | ||
| <td>n/a</td> | ||
| <td>n/a</td> | ||
| <td>n/a</td> | ||
| </tr> | ||
| <tr> | ||
| <th>MacOS</th> | ||
| <td>Mojave</td> | ||
| <td>70.0</td> | ||
| <td>63.0</td> | ||
| <td>n/a</td> | ||
| <td>n/a</td> | ||
| <td>Not supported</td> | ||
| </tr> | ||
| <tr> | ||
| <th>Windows</th> | ||
| <td>7 and 10</td> | ||
| <td>70.0</td> | ||
| <td>63.0</td> | ||
| <td>Not tested</td> | ||
| <td>Not supported</td> | ||
| <td>n/a</td> | ||
| </tr> | ||
| </tbody> | ||
| </table> | ||
| </div> | ||
|
|
||
| <div class="label">I have ran into a problem with MetaDome, what can I do?</div> | ||
| <div class="box"> | ||
| Although we have extensively tested MetaDome and are constantly monitoring | ||
| the server for any downtime. If you do encounter problems or behaviour you | ||
| did not expect. We would highly appreciate it if you could | ||
| <a href="{{ url_for('web.contact') }}">contact us</a>. | ||
| </div> | ||
|
|
||
| <div class="label">On what data are the results in MetaDome based?</div> | ||
| <div class="box"> | ||
| MetaDome combines data from various public resources. The underlying data | ||
| of MetaDome currently contains information from 56,319 human transcripts | ||
| (<a href="https://www.gencodegenes.org/" target="_blank">GENCODE</a>), | ||
| 71,419 <a href="https://pfam.xfam.org/" target="_blank">Pfam</a> | ||
| protein domain instances, 12,164,292 population-based genetic variants from | ||
| <a href="http://gnomad.broadinstitute.org/">gnomAD</a>, and 34,076 pathogenic mutations from | ||
| <a href="https://www.ncbi.nlm.nih.gov/clinvar/" target="_blank">ClinVar</a>. | ||
| </div> | ||
|
|
||
| <div class="label">How often is the underlying data updated?</div> | ||
| <div class="box"> | ||
| Currently MetaDome requires a manual reannotation of the underlying data. | ||
| In a future version of MetaDome is expected to schedule automatic downloading | ||
| of new data releases and automatic reannotation. | ||
| </div> | ||
|
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|
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| <div class="label">Is MetaDome still under construction?</div> | ||
| <div class="box"> | ||
| MetaDome is final for its first release version. But we are still actively | ||
| attempting to improve MetaDome based on feedback. If you have any improvement | ||
| ideas, please <a href="{{ url_for('web.contact') }}">contact us</a>. | ||
| Current improvements that we are working on may be found | ||
| <a href="https://github.com/cmbi/metadome/issues">here</a>. | ||
| </div> | ||
|
|
||
| <div class="label">Why can I not select my gene / transcript for analysis?</div> | ||
| <div class="box"> | ||
| For sake of high data quality we have limited the possible transcripts and genes | ||
| suitable for a MetaDome Analysis to the <a href="https://www.gencodegenes.org/" target="_blank">GENCODE</a> | ||
| Basic transcripts of which the translation is identically matched with a | ||
| <a href="http://www.uniprot.org/" target="_blank">SwissProt</a> protein | ||
| sequence. All GENCODE Basic transcripts are validated to be expressed as mRNA | ||
| and all SwissProt proteins are curated by experts. | ||
| </div> | ||
|
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||
| <div class="label">I cannot find the domain that should be in my gene of interest?</div> | ||
| <div class="box"> | ||
| All annotated protein domains in MetaDome result from | ||
| <a href="https://pfam.xfam.org/" target="_blank">Pfam</a>. | ||
| Pfam holds a strict notion on what a protein domain is and differs to | ||
| other protein domain annotation services. We have specifically chose Pfam, | ||
| as the underlying method is suitable to indicate homologously identical | ||
| positions across protein domains that can directly be used to transfer variant | ||
| information. | ||
| </div> | ||
|
|
||
| </div> | ||
|
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| <h3 class="title" style="color: #00AFDC;">Interpretation of a MetaDome analysis</h3> | ||
| <div class="box"> | ||
| <div class="label">Why are there black boxes in the meta-domain landscape?</div> | ||
| <div class="box"> | ||
| The black boxes represent positions that cannot be aligned to the Pfam | ||
| domain consensus. For these positions we | ||
| cannot transfer variant information across homologous domains. | ||
| </div> | ||
|
|
||
| <div class="label">How is the tolerance landscape computed?</div> | ||
| <div class="box"> | ||
| The tolerance is computed as a from missense over synonymous | ||
| variant count ratio, which is calculated in a sliding window manner to | ||
| provide a per-position indication of regional tolerance to missense variation. | ||
| The variants are based on gnomAD and corrected for codon composition. | ||
| For more information we suggest reading | ||
| <a href="{{ url_for('web.method') }}#tolerance_computation">"Computing genetic | ||
| tolerance and generating a tolerance landscape"</a>. | ||
| </div> | ||
|
|
||
| <div class="label">What do the tolerance landscape' colours indicate?</div> | ||
| <div class="box"> | ||
| The colours are based on missense over synonymous ratio computations | ||
| over the entire protein for all proteins. Here the Yellow (or neutral) | ||
| is based on the average missense over synonymous ratio score that you | ||
| would obtain this way and the red (intolerant) and blue (tolerant) are | ||
| based on the top/bottom scores. | ||
| </div> | ||
|
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| <div class="label">For meta-domain information in the positional information, what does the alignment coverage mean?</div> | ||
| <div class="box"> | ||
| This corresponds to how many homologous positions are aligned to that | ||
| specific position. In general we would advise to maintain a minimum of | ||
| 80% alignment coverage for high quality results. | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </section> | ||
| </div> | ||
| </section> | ||
|
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| {% endblock %} {% block js %} {% endblock %} |
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