18 years of server hosting with the Faculty of Science IT Unit ends in 2016!

In 1999, I attended a two hour html class at Faculty of Science’s CITA, conducted by Frederick H. Willeboordse and assisted by Keith Phua. Each of us in the class was setup with a personal server hosted by the Faculty of Science and I was taught a few common HTML commands and very importantly, FTP.

With hosting solved, I experimented with my site to gain confidence. Soon NUS was granting all my domain requests to setup several websites. Anything was possible, it was just a matter of having enough time. It was the Dropbox, Google Drive and WordPress of that time. Some highlights are reflected here.

Today, the cloud has eased the process incredibly and I am fascinated – last week, from the bus, and with just my handphone, I was able to send my student’s theses to a colleague minutes after he emailed!

Well, today, I received the email I had been warned about – the Faculty of Science IT Unit (ITU) will cease its web hosting service from 31 Oct 2016!

So the probable plan off the top of my head is:

  1. Coastalcleanup.nus.edu.sg – likely merge with the existing coastalcleanup.wordpress.com. Critical pages are already have coastalcleanupsingapore.org subdomains, so I will update those.
  2. Sea.nus.edu.sg – shift some material to LKCNHM webpage or a subdirectory in sivasothi.com
  3. Staff.science.nus.edu.sg/~sivasothi/ (aka sivasothi.com) – shift to external host
  4. Mangrove.nus.edu.sg – subdirectory in sivasothi.com
  5. Chekjawa.nus.edu.sg – subdirectory in sivasothi.com
  6. Habitatnews.nus.edu.sg
    • blog content to blog.nus.edu.sg or wordpress
    • html pages to subdirectory in sivasothi.com
  7. Otter.nus.edu.sg – http://blog.nus.edu.sg/sgotters/ (is setup, just populate)

It is going to be tough, so I imagine I’ll go slow and steady:

  1. Update my local backups to be ready for transfer (mostly done).
  2. Find out about domain mapping to new host.
  3. Minor housekeeping to see what can be archived as pdfs into an indexed Dropbox folder.
  4. Shift the html pages, especially the guidebooks, magazines and bibliographies to the new sivasothi.com server.
  5. Shifting the Habitatnews (2003-2016) blog posts will be tough and will have to queue with Raffles Museum News II (2004–2007) project. Defunct image hosting servers like Skitch caused the most trouble,sigh!

I will try to get some help, and have some fun with this. There is still lots of precious information in there.

It was inevitable this day would come and it has happened later rather than sooner – thanks to the Faculty of Science, and especially Keith Phua, for 18 years of internet freedom!

MailMerge a pdf book of abstracts from submitted project titles and abstracts

NewImageIn modules LSM1303 Animal Behaviour, LSM2251 Ecology and the Environment and GEM1917 Understanding & Critiquing Sustainability, students present project results in a symposia. A pdf book of abstracts is prepared for use during the symposia from title and abstracts recruited earlier using a Google Form.

I allow students very close deadlines, such as the Sunday before a Monday symposium, even if some editorial work is required! This is because the pdf book of abstracts can be generated in minutes, based on student submissions through a Google Forms document. Once the deadline is reached, an Excel version of the Google Forms responses is downloaded and processed.

I have been using the Mail Merge > Catalog function in Word 2011 for Mac to do this, but need to teach others to do this. It is likely that some will be using Word 2016 for Mac, and when I took look, it wasn’t all that straightforward. Online resources helped me figure it out, so I’m listing the steps here for my friends, and also for myself, for the next time I prepare this.

  1. Download the Google Forms data as an Excel File and ensure the following field are available:
    • Group Number
    • Full name of person submitting abstract
    • Project Title
    • Project Abstract
  2. Verify the group number using Excel’s VLOOKUP against the module database of group members and project numbers (overcomes submission mistakes)
  3. Use Excel’s VLOOKUP to extract the proper full names of all group members from the module database
  4. Close the Excel file of abstracts
  5. Open a new document in Word 2016 for Mac, and select the “Mailings” ribbon
  6. Select Start Mail Merge > Directory (this provides a continuos flow of records for the book of abstracts, instead of section breaks between records in a letter mail merge)
  7. Start Mail Merge > Directory – to obtain a continuous flow of text
  8. Select Recipients > Use An Existing List… (select the excel file of abstracts)
  9. Select Recipients > Use an Existing List… – select your Excel file of abstracts

    Selecting my Excel file of abstracts

  10. You will be warned to only open a known file, and prompted to open the workbook
  11. Use “Insert Merge Field” to build the output document template, by inserting text and fields. e.g. Group No. «Group_Number»: – inserts the words, “Group No.” before the point at which the number is inserted.
  12. Apply formatting as needed (e.g. bold, change font size)
  13. Appearance of the Mail Merge template, after inserting text and fields
    Screenshot 23

  14. Specify the Merge Range (if the workbook range was not restricted, specify a range to prevent junk at the end of file. E.g. a range of 1 to 40 if there are not more than 40 records (groups)
  15. Finish and Merge > Edit Individual Documents…
  16. Save the Word document, edit as wanted and print as a PDF

The book of abstracts took minutes to generate. You’re on your own for editing, though!Screenshot 24

After using the Mailings ribbon in Word for Mac 2016, I realise the buttons are arranged logically for the task. And instead of “Catalog” what I was wanting was a “Directory”. So once the teething blues are over (and the angst online from 2015 mostly reflects this, I suspect), I’m back in business!

It is a useful practise to only edit submissions at the source, i.e. in the Excel file. If improved abstracts are invited (through a Google Form), or a second round of editing is exercised by a colleague, the new pdf can be quickly generated by the Word template, and the entire outout be cut and paste into a webpage (see Sustainability Symposium in Singapore).

Efficiency means lecturers can maximise the time available to students to write their abstract, which naturally improves significantly, the closer they get to their presentation date. It isn’t easy writing an abstract and further analysis of fresh work will introduce refinements. This applies to participants at higher level symposia too. Since generating the abstract booklet is fast, I always afford speakers the opportunity to provide revised abstracts right up to the day they speak, so that the permanent record on the web is the best possible version they could have wanted.

So the same techniques will be applied at the 13th International Otter Congress, 3rd – 8th July 2016 in Singapore.

First rule of coastal cleanups – be safe!

This morning, Ivan Kwan reminded Toddycats on our LINE chat to be careful when picking up trash. Our shores are host to venemous animals and they can be nestled anywhere. Coastal cleanup veterans Quek Kiah Shen and Amy Choong responded with memories not of animals but of “sharps and needles” and syringes in Buloh and Lim Chu Kang mangroves in the north-west of Singapore.

Typically during September’s International Coastal Cleanup, volunteers remove 30 –150 syringes a year, but these are mostly from our recreational beaches at East Coast Park and Changi and not from mangroves. Around the world, cleanup organisers warn participants to be careful at beaches, because of the recreational drug users who litter. Even if syringes are empty and washed out so not a hygiene threat, briefings emphasise safe handling and disposal.

However, we are finding instances of numerous syringes in bags, on our north-western shores. These we suspect were dumped offshore. In 2014, this was highlighted at the pre-National Day mangrove cleanup at Lim Chu Kang, where we found, sitting on the shore, a bag of hypodermic needles.

A bag of hypodermic needles on Lim Chu Kang by Chua Li Shan (2011)

Ria elaborated about the larger issue of indiscriminate trash disposal and the presence of numerous offshore fish farms in the Johor Straits. The trash causes a lot of impact to ecosystems, and costs a lot of money to cleanup. Addressing the issue at the source would be great way to prevent senseless damage – read her post which summarises the issue.

Finding a bloody syringe, though, is uncommon, In 2011, Kate Thome reported one from a cleanup at Kranji mangrove. It was rare enough for the ICCS founder leading that cleanup to send me this photograph below. Years of earnest, pre-cleanup safety briefings was put to the test!

The bloody syringe at Kranji mangrove by Kate Thome (2011)

Well, the safety preparedness paid off for the students who found the syringe calmly kept a distance and called an adult over. It was photographed and disposed in hard plastic, so that no garbage worker would be accidentally pricked on its way to incineration.

I tweeted that image and reporters Jalelah Abu Baker and Kimberly Spykerman picked up the news and wrote an interesting story for a general audience. We circulated it to Organisers as a reminder to be prepared and vigilant.

Registration for Organisers for September’s data gathering International Coastal Cleanup has begun. As coordinators prepare Organisers, we suggest they adopt ICCS’ “Advice for Participants” and by circulating the pdf early and covering the points during the on-site briefing, just before their cleanups begin.

Just like we will do so at Operation We Cleanup Up on Sunday 8th May 2016.

The Advice for Participants can be read off a handphone, and include these statements, which have been made more explicit over the years:

  • Place your feet carefully on the ground – beware of broken glass, fishing hooks, syringes and other sharp objects which may be present on beaches. Fish such as stingrays and catfish have sharp spines.
  • Examine items carefully before picking them up – sharp objects can pierce your gloves.
  • Do not use your feet to kick or feel objects.
  • Dispose of glass and sharps (e.g. syringes) responsibly – pad them well with numerous empty plastic bottles and dispose these separately in canvas trash bags – workers who transport trash bags later to waste incineration sites must be protected from accidents. Alert your Organiser.

In the months leading to the cleanup, we will emphasise safety above all else. We tell Organisers every year that it doesn’t matter if they mess up data collection, or report late, or forget to take photos, or are unable to eliminate the trash (there are other cleanups), the first rule of coastal cleanups is and has always been – be safe!

Not by honours thesis alone, also by internship and coursework – three ways to fulfil the Life Science Level 4000 requirements

This honours research module is a familiar rite of passage for all honours students and numerous students have learnt and contributed this way for decades.

In terms of modules and credits, to fulfil the Level 4000 requirements for Life Sciences Major, an undergraduate is presently required to pass

  1. LSM4199 Honours Project in Life Sciences [16 MCs], and
  2. Four LSM42xx elective modules [4 x 4MCs].

The Department of Biological Sciences which hosts the Life Sciences Undergraduate Programme issued the notice, “Changes to Life Sciences Major Level 4000 Requirements (1st April 2016)” [link]

We have been discussing this for some time now, as the honours cohort is expected to increase in light of the changed CAP cut-offs for honours, which were announced in 2014. Research lab space is strained and we need different strokes for different folks. So it is nice to see this finally announced.

There are a now three ways to fulfil the Level 4000 Life Science requirements:

  1. Honours Research Project (no change) – i.e. Pass LSM4199 + 4 LSM42xx elective modules
  2. Applied Internship Project – Pass LSM4299 Applied Project in Life Sciences + 4 LSM42xx elective modules
  3. Coursework; pass 8 LSM42xx elective modules.

This is applicable to students reading Life Sciences as primary major of the following matriculation cohorts

  1. AY2013/2014 – Current Year 3
  2. Cohort AY2014/2015 – Current Year 2
  3. Cohort AY2015/2016 – Current Year 1

Read the complete document at LSUP, which includes a description of the new LSM4299 Applied Project in Life Sciences, a full-time, “six‐month‐long project in an applied context that culminates in a project presentation and report.”

Update – read the five-page description for LSM4299 Applied Project in Life Sciences

Removing that vulnerable Java browser plugin (and Flash) on OSX

Do you still have Java on your OSX desktop? Look for it in System Preferences. If you do, you should have received regular reminders to update the software, which I hope you have followed. This is because flaws in Java are regularly targetted and these updates are critical for the security of your Mac.

In 2013 in particular, the Java browser plug-in (and not Javascript) was loudly condemned for its insecurities. Most IT magazines recommended removing Java altogether.

By OSX 10.11 El Capitan, a clean install would have removed both the Java Runtime Environment (JRE) and the Java Software Development Kit (JDK).

Users who still need to use an app or webpage requiring Java may be prompted to install the software. Apple suggests downloading the current version of Java for OS X directly from Oracle, or the legacy (unsupported and out of date) Java SE 6 from Apple (see also the instructions at OSX Daily). But Oracle, which ships the Java installer for OSX, can be infuriating, shipping ask.com adware with the installer.

Java was installed on my Mac Book Pro, for a reason I now forget and when I was prompted yet again to upgrade, the nstaller tried to slip in Yahoo search as a default on my browser. Irritated, I checked the links above and deleted the files or directories in the following areas:

  1. /Library/Internet Plug-Ins/JavaAppletPlugin.plugin
  2. /Library/Java/JavaVirtualMachines/
  3. /Library/PreferencePanes/JavaControlPanel.prefPane

I do use CrashPlan 4 which requires Java, but JRE is packaged with the app and is not affected by the deletions – a restart confirmed this.

Is Java insecure? No, it is the web browser plug-in which is vulnerable and this is enhanced by poor housekeeping. A peek in /Library/Internet Plug-Ins/ of my intern revealed both an out of date Java plugin and Flash residing there. She had that sorted that out promptly, and you should too.