wurmlab / wurmlab.github.io Goto Github PK

(ideally a reduced version) https://publons.com/author/484224/widget/embed/

this is shown on my mac, using firefox, and chrome

THis is a bad thing says analytics:

Optimization Suggestions
Eliminate render-blocking JavaScript and CSS in above-the-fold content
Your page has 4 blocking CSS resources. This causes a delay in rendering your page.
None of the above-the-fold content on your page could be rendered without waiting for the following resources to load. Try to defer or asynchronously load blocking resources, or inline the critical portions of those resources directly in the HTML.
Optimize CSS Delivery of the following:

https://maxcdn.bootstrapcdn.com/…ootswatch/3.3.6/flatly/bootstrap.min.css
https://fonts.googleapis.com/css?family=Lato:400,700,400italic
https://netdna.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.css
https://wurmlab.github.io/css/custom.css

Furthermore, we should put a browser cache date on images and css (not on content) - currently everything that is more than 10minutes old gets redownloaded

Leverage browser caching
Setting an expiry date or a maximum age in the HTTP headers for static resources instructs the browser to load previously downloaded resources from local disk rather than over the network.
Leverage browser caching for the following cacheable resources:

Dear both - there seem to be some stray tags here?
wurmlab.github.io/team

d61ec67

https://www.checkbot.io/

is very good

• "The Molecular Clockwork of the Fire Ant Solenopsis invicta" : "/publications/ingram2012-fireAntClockGenes.pdf"
• "Epigenetics: The Making of Ant Castes" : "/publications/2012CurrBiolAntepigenetics.pdf"
• "Odorant Binding Proteins of the Red Imported Fire Ant, Solenopsis invicta: An Example of the Problems Facing the Analysis of Widely Divergent Proteins" : "/publications/gotzek2011obps.pdf"
• "Behind the Scenes of an Ant Genome Project" : "/publications/wurm2011antGenomeBehindTheScenes.pdf"
• "Parasitoid Wasps: From Natural History to Genomic Studies" : "/publications/wurm2010wasps.pdf"

add

wurmlab.github.io/calendar.html is not found?

The link to the SIB Bioinformatics & Population Genomics course is broken, it needs to be updated or removed. I cannot find an updated link, does anyone have it?

• Proc B is inconsistently named
• <br> should be <br/>

So perhaps we should include local copies of all libraries?

is it safe to delete the extra branches? If so please do so
thanks,
Yannick

There are two problems in the implementation of the folding/unfolding feature:

First, the [Abstract] button has extra space to its left compared to others ([PDF], etc.)

Can be fixed by adding display: inline to .lbl-toggle style in custom.css.

Second, the implementation assumes that all papers will have a doi attribute - would be a good idea to check that all papers have a doi attribute indeed. Without the doi attribute, the [Abstract] button will still be rendered but it won't work. As a potential safeguard, one can check if the paper has both abstract and doi keys (in line 741) before rendering the [Abstract] button.

Alternatively, one can strip space from title attribute and use that or use MD5 hash of the title.

From #95

... with image on the left. Will generate more room for the image and text.

http://wurmlab.github.io/team is loop infinitely for me…

Anyone else?

@nat2bee asked me how the index/3-min journal club worked. I explained quickly, maybe other labs might want to read this too. We could write a short post about it, and share the R code as well.

This is a change in the config file…

I suggest this because {{site.url }} currently defaults to http:// despite whether or not http:// or https:// is used.

As a result, if you are viewing the website at https://wurmlab.github.io, the links in the header takes you to the http:// links…

BTW: using HTTPS has a major impact on SEO according to Google

I think this an API change rather than our breaking it

IIRC its currently set at 10 minutes

for everything other than html files it could be longer... e.g. 1 month.
https://developers.google.com/speed/docs/insights/LeverageBrowserCaching
https://developers.google.com/web/fundamentals/performance/webpack/use-long-term-caching

After SequenceServer and Afra, and before oswitch perhaps.

@IsmailM

Maybe add something more recent?

Alignment of titles is heterogeneous (e.g. on the attached screenshot, the 3rd, 4th and penultimate publication are right-shifted by a space)

Just received the following notification from Github:

You are currently using the 'rdiscount' Markdown engine, which will not be supported on GitHub Pages after May 1st. At that time, your site will use 'kramdown' for markdown rendering instead. To suppress this warning, remove the 'markdown' setting in your site's '_config.yml' file and confirm your site renders as expected. For more information, see https://help.github.com/articles/updating-your-markdown-processor-to-kramdown.

/cc @EmelineAurore

Can we get a travis setup going to check for html and css validity?

In the same way blink tags are annoying. A static image would be much better.

The below are links identified by google that are present on the internet linking to a non-existing page on our website.

Once these are 'fixed', the relevant link needs to be marked fixed on the Search Console.

https://wurmlab.github.io/news/2014-01-15-vacancies/

LINKED FROM:

• https://wurmlab.github.io/atom.xml
• https://wurmlab.github.io/news/2013-12-22-news/
• https://wurmlab.github.io/news/
• https://wurmlab.github.io/news/2014-01-27-reference/
• http://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/news/archive/

LINKED FROM:

• https://wurmlab.github.io/
• http://wurmlab.github.io/sitemap.txt

LINKED FROM:

• https://wurmlab.github.io/teaching/2014sbc322/methods/index.html
• http://www.librospdf.net/biologia-celular-smith-y-wood---completo/4/

LINKED FROM:

• https://wurmlab.github.io/news/2015-03-16-bioinformatician/
• https://wurmlab.github.io/sitemap.txt
• http://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/news/archive/

LINKED FROM:

• https://wurmlab.github.io/sitemap.txt
• http://wurmlab.github.io/sitemap.txt

LINKED FROM:

• https://wurmlab.github.io/atom.xml
• https://wurmlab.github.io/news/2015-02-05-scientific-writing/
• https://wurmlab.github.io/news/
• https://wurmlab.github.io/
• http://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/news/archive/

LINKED FROM:

• https://wurmlab.github.io/atom.xml
• https://wurmlab.github.io/news/2015-02-05-scientific-writing/
• https://wurmlab.github.io/news/
• http://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/news/archive/

LINKED FROM:

• https://wurmlab.github.io/news/
• https://wurmlab.github.io/sitemap.txt
• http://wurmlab.github.io/sitemap.txt

LINKED FROM:

• https://wurmlab.github.io/sitemap.txt
• http://wurmlab.github.io/sitemap.txt

LINKED FROM:

• https://wurmlab.github.io/sitemap.txt
• http://wurmlab.github.io/sitemap.txt

LINKED FROM:

• https://wurmlab.github.io/atom.xml
• https://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/news/
• https://wurmlab.github.io/news/2014-10-31-recruiting-population-genomicist/
• http://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/news/archive/

LINKED FROM:

• https://wurmlab.github.io/news/2015-03-16-bioinformatician/
• https://wurmlab.github.io/news/2015-02-05-scientific-writing/
• http://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/news/archive/

LINKED FROM:

• https://wurmlab.github.io/teaching/2014sbc322/methods/index.html

LINKED FROM:

• https://wurmlab.github.io/teaching/2014sbc322/methods/orthologs.pdf

LINKED FROM:

• https://wurmlab.github.io/sitemap.txt
• http://wurmlab.github.io/sitemap.txt

LINKED FROM:

• https://wurmlab.github.io/sitemap.txt
• http://wurmlab.github.io/sitemap.txt
• https://wurmlab.github.io/team/index.html

LINKED FROM:

• https://wurmlab.github.io/news/2014-07-30-2014-07-30-recruiting-population-genomicist/
• https://wurmlab.github.io/news/
• https://wurmlab.github.io/news/index.html

LINKED FROM:

• https://wurmlab.github.io/news/2016-04-25-googlesummerofbioinformaticscode/

LINKED FROM:

• https://wurmlab.github.io/news/2016-04-25-GoogleSummerOfBioinformaticsCode/

LINKED FROM:

• https://wurmlab.github.io/news/

LINKED FROM:

• https://wurmlab.github.io/teaching/2014sbc322/methods/
• https://wurmlab.github.io/teaching/2014sbc322/methods/index.html

LINKED FROM:

• http://genevalidator.sbcs.qmul.ac.uk/
• wurmlab/genevalidatorappAPI#8

LINKED FROM:

• http://genevalidator.sbcs.qmul.ac.uk/

There are only links to 4/5 practicals
There is no link to the 3rd Practical on Gene Prediction
Practical 3 link leads to 4th Practical on Variant calling
Practical 4 link leads to 5th Practical on Popgen

http://www.antgenomes.org/~yannickwurm/tmp/linklint/index.html

• register our bioinformatics tools in https://bio.tools
• ensure our publications are uploaded and accessible where appropriate (academia, mendeley...)

From #35.

Justified text is prettier to look. I think it will look great with magazine style layout of the home page.

• move diego to alumni
• add fabio (shorten his blurb)
• add page for yannick

• update sequenceserver paper and include supp
• add genevalidator chapter @yeban
• move old people to alumni
• news item about social evolution course and conferences?

blog posts needed. Please comment when you are planning to publish so we don't publish all at the same time, it will spoil the fun.

• New publication - can @MartinezRuiz-Carlos or @roddypr or @yannickwurm write a blob about this? This is the top priority, needs to happen very soon to keep the momentum
• conferences and workshops over the last four months, can you do that @MartinezRuiz-Carlos ?
• Google Summer of Code blog post from @aniarya82 ?
• Masters and Undergrad students - I will do this
• comparison of library preps - I will do this
• anything else?

Autogenerate similar to tools / teams page. Important: DOI & PDF links, citations count.

Probably following this:
https://help.dreamhost.com/hc/en-us/articles/215089118-Adding-an-SSL-certificate-overview

with new design:

• too much vertical whitespace on tools page
• too much vertical whitespace above headings on news page
• too much vertical whitespace on tools page
• home page: too much whitespace on right side under map. Perhaps this can be filled with the stuff thats currently at the bottom.
• Navigation: publication -> Publication_s_
• home page: too much whitespace between sections
• home page: click on paragraph of relevant section should have same effect as clicking on "read more"
• home page: "read more" buttons mean we need a lot of whitespace - need a better solution.
• home page: pollinator "read more" button for one line is an unnecessary complication

• s/Approaches/Approach (I think)
• missing closing paren in the first bullet point

This applies to e.g. our teaching pages (genomics course and R course)
-> they should be better integrated to potentially attract people to rest of the site.

at bottom of news page the link to http://wurmlab.github.io/news/archive.html is broken