Posting guidelines

The following is a set of guidelines to follow when adding new blog posts or calendar events. If followed, it will allow multiple authors to produce content for the website with a consistent style.

Blog posting guidelines

WordPress uses tags and categories to allow you to make blog posts appear in different places and also make it easier for others to only view certain types of blog posts. Over time, the number of tags and categories used on the Genome Center website has been reduced, in an effort to keep things as simple as possible.

Currently used blog categories

Example showing how to flag blog posts with categories or tags

Example showing how to flag blog posts with categories or tags (click to enlarge)

By default all posts appear in the News category. This reflects the fact that just about every post that is made on the website represents some form of Genome Center news (new paper, new coverage of the Genome Center by the media, new event etc.).

The choice of category is controlled by settings on the right-hand side of the blog editor page (see image on the right, though note that this also shows an Events category that is no longer used). All posts that are placed in the News category will appear here and the 10 most recent items will appear on the news page.

The only other category to consider using is the Highlights category. These are for the most newsworthy of posts, and the five most recent Highlight posts will additionally appear on the front page of the website (this ensures that the list will never grow too long). Highlights is a subcategory of news.

You may wish to sometimes use Highlights as a way of temporarily bringing extra attention to a news item or event. E.g. imagine that we receive some last-minute notice about a talk that’s happening either at the Genome Center or somewhere else (but involving a Genome Center member). In this case we could create a new blog post which is categorised as a News item (the default category) and also as a Highlight. This gives it some extra prominence by making it appear on the home page of the website, but perhaps after the talk has passed we would remove the blog post from the Highlight subcategory.

On all website pages, apart from the home page, there is a widget in the bottom of the sidebar which shows how many posts have been made in each category. You can click on these counts to see all posts in that particular category.

Currently used blog tags

I use the following two  tags to flag blog items if they relate to a few specific topics:

  1. careers — for job postings
  2. videos — for any post that contains a video

I suggest that this is probably more than enough to manage and adding too many tags will get harder to track. These tags make it easier for users to jump from any one post to see other related posts (tag names appear as links at the end of each published blog post). The careers tag is only used for job postings and this means that such posts will automatically appear on the Recruitment page.

Tips for writing news items

News posts will typically reflect some accomplishment from someone in the Genome Center: an interesting and/or prestigious paper, a grant or other funding award, joining/leading a new consortium etc. We will often have an external source of information to link to. When writing news posts I aim for the following criteria:

  1. Just 3–5 sentences about the news item. Basically to introduce the people in the news and a little about why they are in the news.
  2. Link to an external news source when possible. This is especially true if the Genome Center person in question is being featured in an external news item.
  3. Include a quote from the Genome Center member (if they have time). Just 1–3 sentences is fine. Use the ‘block quote’ tool in the editing toolbar.
  4. Include a picture or graphic to go with the story. I’ve started taking simple pictures on my iPhone of Faculty members in their office and then adding them to the post. Alternatively, there may be a logo or graphic associated with a consortium or other organization that is featured as part of the news story. Here is one news piece I wrote about someone receiving an award,  here is one about someone publishing a paper, and here is one about a Grad student being interviewed about their work.

Checking your blog post

excerpt problem

Example of excerpt problem (click to enlarge)

Any blog post will end up on the News page, as well as on the ‘Recent News’ sidebar, and potentially on the website’s home page (for news ‘Highlights’). It is important to note that the News page tries to generate automatic excerpts for each story. These excerpts show the first few dozen words of the story and then appends a Read more… link. You should be aware that the automatic excerpts can sometimes go wrong. This happens if the first part of a news item has a web link,  block quote, or certain other ‘non-plain-text’ content. If this happens, then the problem item can affect all items beneath it on the News page (the individual post is fine if viewed on its own). See image to the right:

In this situation, the block quote of the ‘Test post’ causes the excerpt of the blog post that follows (in the red box) to erroneously adopt the block quote style. To fix this, you must manually add an excerpt to the offending blog post.

Click on ‘Posts’ on the WordPress dashboard, and then on the problem post to edit it. Beneath the main box that holds the content of the blog post, you will notice an empty ‘Excerpt’ box (see below). Simply copy and paste some of the text from the start of the blog post into this box and then click ‘Update’. Your selected text should then appear as an excerpt when viewing the News page.

excerpt problem 2

The excerpt box (click to enlarge)

Event posting guidelines

I have set up a Google calendar under the Genome Center Google account. See the Events page for more details of how to access this calendar. You will need Adam or Keith to share the calendar with you and grant you permission to add entries. For this you will need a Google account.

The Genome Center Events calendar is for events that either take place at the Genome Center (GC symposium, workshops, Foosball tournaments) or which predominantly feature the Genome Center elsewhere (e.g. ‘Evening with the Genome Center’ type events). Talks that happen at the Genome Center can be included on this calendar. I.e. it is mostly intended for people who work at the Genome Center who might want to see if something of interest is happening in the GBSF building, but it should also be of interest to others on campus and further afield.

When adding details of a new event, I have been using the following guidelines:

  1. For seminars and talks, the event name should be ‘Seminar’, an em-dash (—), the speaker’s name,  another em-dash, and then the talk title. Nothing else. E.g. Seminar — Dr. Ian Korf — Bioinformatics solutions for toddlers
  2. For other non-seminar events, try to make it clear what the event is, and include explanatory title. E.g. Workshop — Learning to use Unix and Perl
  3. Date, and start and end times of talk should always be provided.
  4. Location field should be used to list room and building on campus. E.g. ‘1022 Life Sciences, UC Davis, Davis, CA’
  5. The Description field can list other relevant details. E.g. list the seminar series that a talk might be part of, include a URL for a website (if relevant), list the institutional affiliation of any non-UC Davis speaker.
  6. As much as possible, use the Description field (and no other) for all of the extra information. Keep the main title of the event clean and consistent (type of event + name + talk title).

As well as featuring on the Events page, calendar items will appear in the sidebar of webpages. People can subscribe to this calendar in whatever local calendaring app that they use.

Certain Events can, and should, also be created as separate blog posts (flagged in the Events category, and possibly News and Highlight categories). It all depends on how important/prestigious the event is, and how much attention you want to draw to it.

 

 

Upcoming Talks and Events

Events on January 14, 2019
WCMC: Hands-on LC-MS Data processing and Statistics
Starts: 12:00 am
Ends: January 19, 2019 - 12:00 am
Location: UC Davis Conference Center, 550 Alumni Ln, Davis, CA 95616, USA
Description: Registration: http://ucanr.edu/survey/survey.cfm?surveynumber=15575

This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation.

We will instruct using a variety of software, workflows, and algorithms but also give theoretical background information and overviews. We will focus on utilizing open source software and only refer to commercial or vendor software when necessary.

All participants will be trained on laptops that were specifically purchased for course training, with all software already installed and data available to use.

The course will include:

untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
The course fees are $ 2,500 per participant to cover expenses for instructors, organization, materials and meals.

more Info:

Jeannette Martins

email: jmartins@ucdavis.edu

phone: +1-530-754-5357

Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.
Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:


1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.

Categories