Online Teaching and Learning with Zoom-Settings found to be worth zoomed in

As the global outbreak of COVID-19 lead to the closure of the state universities on 13th of March 2020 and subsequently to a lock down across the country, we at the Department of Computer Engineering, University of Peradeniya, Sri Lanka had to move our teaching and learning sessions online. One of the widely used tools for this is the Zoom video conferencing tool made available through Lanka Education and Research Network (LEARN). It is used to conduct synchronous lectures to the students, while asynchronous lectures sharing, and material sharing is done via another effective tool used within the faculty based on Moodle: the Faculty of Engineering e-Learning System (a.k.a FEeLS).

Use of Zoom has enabled conducting interactive lectures, tutorials, lab sessions and meetings of project groups with their supervisors. I happened to be using tools such as FEeLs and Google Classroom for classroom management and tools such as Skype, BigBlueButton for online meetings, and this has been a time when Zoom is being widely used in work, whereas previously it has been for casual meetings among the members of volunteer groups I was involved in.

With my experience so far with Zoom, I strongly believe that it will be a good idea to check on the Zoom meetings settings and have a quick test done before the meeting. Mainly, because you would not want to spend a large amount of an hour-long synchronous session setting it up and housekeeping, and would like to have records of the meetings conducted, and would not want to accidentally miss recording the session as you wanted to. Here, I am listing a set of settings I found to be worthwhile checking and setting up before an online session via the Zoom premium application.  The corresponding settings can be set up through the settings menu in the administration panel (at the top left), once you log into the web portal with your Zoom registered account.

settingspanel

Menu at the top right of the administration web portal in Zoom

  1. Enable Recording of the session

Recording of sessions is supported via the Zoom desktop client and is not available via the browser.  The session recordings can be set to be saved in the cloud or the  local machine.

recording-tab

2.  Maintaining the chat history

If you would like to have a record of the chat during the session, it has to be turned on via the same panel (as Recording )above.

3.  Meeting control tool bar

For a smooth experience for the participants, it will be worthy to familiarise yourself with using the meeting control tool bar, while you are recording a session or sharing the screen. This setting can be viewed under Settings (at the top right in the administration web portal)-> Meeting

4. Virtual background

This is an interesting feature from Zoom supported in the Zoom desktop client. This allows us to have a virtual background of our preference for our video. This may be useful if you would like to have a background different from your living room set up or/and add some fun to the session. One of the default backgrounds provided from Zoom makes you look like presenting from space! It is recommended to use a green virtual background for a better video.

setting3 (2)

 

5. Use a password for the meeting and share it separately (via SMS, Whatsapp messaging, etc)

For each meeting, a password can be set up and it can be shared by other means of communication. This setting is available for each meeting listed under the Meetings menu (at the top right in the administration web portal).

6. Retrieving records of completed meetings

Reports of online sessions conducted via the Zoom desktop client including attendance are available under Reports (at the top right in the administration web portal). This feature is not available for meetings conducted through the web client.

7. Personal Meeting room

This feature enables us to have our virtual meeting room which can be dedicated to regular/frequent visitors. It can be used to launch instant meetings or/and as a convenient method to set up routine meetings, for which all that is required is to share the personal meeting room id with the intended participants. With that, the invitees will be able to join (pop into our virtual meeting room) anytime unless  the meeting is locked or the waiting room feature is setup. This is available with the Zoom web, with the Zoom Desktop Client, or with the Zoom mobile app.

A comprehensive guide on setting up a personal meeting room in Zoom is available here.

8. Join before host

This enables the participants to join the session before the host starts or joins the session. This will be useful if you are setting up a meeting for someone else. This setting is available under Edit Meeting option selected for any meeting from the Meetings menu (at the top right in the administration web portal).

Online learning and teaching with Google Classroom

Google classroom is a user-friendly easy-to-learn tool for classroom management. With my experience with Google Classroom with a class of 420 Engineering undergraduate students and at a couple of small classes, I am unable to recommend it as a complete alternative to a fully-pledged learning management system (LMS) like Moodle.

I have encountered a couple of glitches with Google Classroom and mainly miss the feature of having a discussion forum (grouped under topics).  Nevertheless, given it comes with the support of other Google Apps, and the students would probably be comfortable with using those apps, it can be an effective tool for online classroom management, including formal assessment.

The slides from a short session that I conducted to a group of academics on Google Classroom is here. The first slide acknowledges Google(lk) commemorating the independence day of Sri Lanka which falls on February 4th.

A day with school kids at Nugagolla Central College, Wilgamuwa

On 28th of November, Nugagolla Central college had their first ‘Kala Ulela’ at the school, I am so glad that we could join them with presents. These presents were from a group of us from 2007 class of Girls’ High School, Kandy.

I felt honoured to have the opportunity to share a few words with the college students at the event at their first Sinhalese Literature day, and share my experiences at the University of Peradeniya. I hope I could inspire them to pursue their dreams and keep their passion for Arts and Culture.

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An Evening at Seth Madura

Seth Madura located close to Galmaduwa temple, Kundasale is a home for 17 children with special needs. A bunch of flowers seeking sunlight to shine they are..

On November 9th 2019 evening Seth Madura had visitors and they all had a nice evening together. With  the effort of the children and the staff the place is well maintained and they love talking of their work at school.
Your presence will be warmly welcomed by them and we invite you to visit them
https://goo.gl/maps/SpA9NJnD25bqyPtw6

This post is written in gratitude to all who shared this happiness with their contributions and presence and also to Seelagawesi Thero for making us aware on this place.

This was the first project by Dhara foundation, a group formed to help children with special needs around Sri Lanka.

With love from Melbourne, Australia to Hatton, Sri Lanka : The book donation

While I was a graduate student at the University of Melbourne, Australia I had the idea of  sharing books from Melbourne to Sri Lanka, from ones who are no longer reading (a book) to ones who are in need of reading (the same). I shared this idea within my circle and a couple of people were happy to contribute.

Making that idea fruitful I was able to collect 41 childrens’ books.  They were donated to a library at Sri Pada college, Hatton on 15th of November 2019, as a part of a book donation project.

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So happy and grateful that I could contribute to this task.

 

 

Thinking in design patterns- GRASP

It is essential for a software engineer to develop the ability to think (and communicate) in terms of design patterns. The fundamentals of design patterns can be explained based on GRASP : General Responsibility Assignment Software Patterns (or Principles).

A set of slides presented by me to a group of software engineers (including interns) summarising GRASP is here.

They are adopted from the book: Applying UML and Patterns: An Introduction to Object-Oriented Analysis and Design and Iterative Development by Craig Larman.

AGTA Conference 2018 : Microbes, Computer Science, locals and beaches

I was soo glad to be in Adeleide this November to attend the Australasian Genomics Technologies Association. I am also thrilled to have received two awards at the conference: AGTA Travel award and AGTA Best Poster award. 20181107_22084745407024_10215296800786461_4616739502717665280_o

The conference this year was filled with informative talks and discussions. It also had the participation of researchers working in molecular biology, and computational biology from all states of Australia and from countries outside the Australia including France and the USA.

කතා දෙකක කතාවක්

මම තනියම වෙන රටකට ගිය වෙලේ මාව ගෙදර නතර කරගෙන රාජකාරිය ඉවර වෙනකල් මාව බලගත්තෙ නීලා. එයා යාපනේ ඉපදිලා යුද්දය නිසා ත්‍රිකුණාමලයට ආ කෙනෙක්. ගෙදර මිදුලට බෝම්බ වැටෙද්දි, ගෙදරින් ආ හැටි එයා මට කීවෙ තරහෙන් නෙවි, ගෙවුනු කාලෙ මතක් කරන ගමන්..පුංචි කාලේ මාව වඩාගෙන මාත් එක්ක සෙල්ලම් කල මගේ අය්යා කෙනෙක් යුද හමුදාවට බැදිලා සම්පූර්ණ මිනියත් නැතිව ගෙදර ආ හැටි මං කීව. ඊට කලින් දෙවතාවක් ඒ අය්යා නිවාඩුවට ආ හැටි මට මතකයි. අම්මාට සලකන්න රස්සාවක් තිබීම ගැන බොහොම සතුටෙන් ඔහු හිටියේ. ..

මේ කතා දෙකෙන් පස්සෙ මිනිත්තුවක් අපි දෙන්නම නැවතුන, ඒ මිනිත්තුව මට තාම මතකයි.

‘අද රෑට තොසේ??’ අපි පුරුදු කතාවට වැටුනා.

වසරකට කලින් ටික දවසක් මාත් එක්ක නැවතුනු ෆාතිමා මඩකලපුවෙ. දවසකට පස් වතාවක් එයා වන්දනා කරනව, අසුරු සැණක් පාස සිහිය පිහිටවන්නය යි මන් ඉගෙන ගෙන තියෙනව, අවමයෙන් දවසකට පස් වතාවක් සිහිය පිහිටුවන්න පුලුවන් නම් මට ඒක දිනුමක්, ආරිය අට මගට පිවිසීමක්…

මේ අවුරුද්දේ කාලෙන් කාලෙට කලබල අතරේ සමහර අය ලියන, කතා කරන දේ දකින කොට මට මේ සිද්දි දෙක මතක් වෙනව.

බොහෝම කාලයක් අපි බොහෝ දෙනෙකුට එකට ඉදගෙන ඉවසීමෙන් එකිනෙකාගේ කතා කියන්න හෝ අහන්න මොහොතක් නොලැබුණු එක ගැන එතකොට මට කණගාටු හිතෙනව…

Exploiting advancements in genomics in binning – latest work

Combined application of single cell genomics and meteagnomics is identified to be beneficial in improving genome assemblies of uncultivable bacteria [1]. Most of the metagenomic binning methods are hindered by the low abundance of species and have low performances in discriminating sequences of multiple strains [2]. Single cell genomics may aid in overcoming mentioned limitations.

Recent trends in metagenomic sequence binning. 

 

 

Tool Source Features Year published Applications
Autometa [3] https://hub.docker.com/​ r/jasonkwan/autometa sequence homology, coverage, and nucleotide composition 2018 Binning microbial genomes from single shotgun metagenomes. 

Aims to alleviate the requirement to remove host genome prior to analysis-because it is not feasible for non-model hosts

BMC3C [4]

-2018

http://mlda.swu.edu.cn/codes.php?name=BMC3C Composition (4-mer frequency)

coverage

Codon usage

2018 Binning multiple metagenomic samples
DESMAN [5] https://github.com/chrisquince/DESMAN Based on the binning results from a tool working on co-assembly of metagenomes, single copy core genes  (SCG )are used. SCG- core genes that are present in all strains as single copy 2017 De novo extraction of strains from metagenomes

Autometa methodology

A 3 step process

  1. Classify contigs at kingdom level based on BLAST searches
  2. 5-mer frequencies of contigs in each bins are considered. PCA/BH-tSNE is used for dimensionality reduction. The two dimensions from BH-tSNE and coverage information is used for clustering using DBSCAN. The unclustered contigs are recruited back into bins based on marker genes 

Binning tools work on both single metagenomes and based on data from multiple metagenomes. 

 

BMC3C methodology

3 matrices are created.

  1. composition – n x w matrix where n is the number of contigs and w is the number of distinct words (136 for 4-mer frequency)- The matrix is normalised by the contigs length

2 Coverage – n x s where s is the number of metagenomic samples. The matrix is normalised to remove zero entries

3 Codon usage – 5 statistics corresponding to codon usage are considered. A n x 5 matrix

These matrices are concatenated into one with the dimensionality of d = w+s+5

The procedure for binning is 4 steps

 step 1 – Determine the number of clusters

step 2 –  Repeatedly apply k-means clustering

step 3 – Build  a weighted graph –  node corresponding to contig, edge corresponding to frequency of two nodes grouped into same genome bins. 

Step 4- Partition the graph using a graph partitioning algorithm into subgraphs corresponding to a genome bin.

References

[1]Xu, Yuan, and Fangqing Zhao. “Single-cell metagenomics: challenges and applications.” Protein & cell (2018): 1-10.

[2] Herath, Damayanthi, et al. “CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.” BMC bioinformatics 18.16 (2017): 571.

[3] Miller, Ian J., et al. “Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.”bioRxiv (2018): 251462.

[4] Yu, Guoxian, et al. “BMC3C: Binning Metagenomic Contigs using Codon usage, sequence Composition and read Coverage.” Bioinformatics (2018).

[5] Quince, Christopher, et al. “DESMAN: a new tool for de novo extraction of strains from metagenomes.” Genome biology18.1 (2017): 181.