Tracey Calvert-Joshua
Tracey Calvert-Joshua is a bioinformatician and a PhD student at the South African National Bioinformatics Institute. She worked in cancer genomics, operon prediction and SARS CoV-2 data analysis.
Activity
-
Correct. They are constantly revising the primer schemes and getting better and better at overcoming amplicon dropouts
-
We actually have two several types of Bioinformaticians. Some coming from a background in Biology, others from computer science and some from either Maths or stats. There are obviously more, but these are the main groups I've seen.
But I agree, I've seen many from a non-Biology background make simple mistakes when just jumping into coding, because the...
-
Interesting. QCs are always very important for all steps involving data
-
It really helps to cement it when you see how to use it practically.
-
Tracey Calvert-Joshua replied to George Msuku
Great. You have just discovered a gold mine (**,)
-
Can you explain what you mean? A virus is either DNA or RNA, but obviously its genetic content is vastly outweighed by the larger host's. So, we normally have to do something like amplicon-based sequencing so that we can specifically increase the viral content.
-
I love this!! I always said this this was my appeal when it came to Bioinformatics. It appeals to my chronic questioning of everything, while satisfying me with quick answers. No stress about an experiment that failed and having to wait forever for reagents, etc.
I also enjoy the mathematical underlying, which means that trail-and-error is more logical,...
-
Generally, if you have enough skill with programming (high-level language and bash scripting), you have a dedicated server with enough storage space, etc. and you have a good technical support group, then you can manage.
For some tools, Galaxy does not make all the options/parameters available, because there are just too many, and obviously one of the aims...
-
It's just one of those things where it's initially overwhelming, but the gaps get filled in the more you do it.
-
@CynaraCarvalhoNunes, the burger items are right at the start of the article/tutorial. You will get an empty file if you did not copy these items and paste them into that block as allocated, and changed the file type to ".txt"
-
It's often a lie our mind tells us, because one can never be fully prepared for the unknown anyway. So, you start and then you guage how much energy, time or research will be required at each step of the way.
In fact, the very reason why we remain unprepared, is because we never started.
Ask your mind, if it's really due to being unprepared, then why am...
-
I'm sure you'll get there in no time.
-
The tutorials are a good place to start. Very informative and comprehensive.
-
Wow awesome. I believe you may be our first teacher.
-
There are definitely two groups of people when it comes to Bioinformatics.
There are labs for whom Bioinformatics makes up a really small part of their research component. This group tends to just want to just get their analyses done, and so, do not wish to have to learn to code and to install and work in Linux.
The second group for sure would want to...
-
From scratch do you mean the tool or the workflow?
-
Yeah, hopefully they will sort out the storage problem soon. I also have an EU account.
-
David, we unfortunately do not have this functionality and this is also not the vision of the course - which encourages social learning.
-
I completely agree. Even as a coder, I still use Galaxy extensively and the tutorials are really well put together. Also, for many of the pipelines, you can also see the Linux and often R and Python scripts for the workflow after it ran - which you can then reuse.
-
The Future Learn platform unfortunately does not allow for image transfers.
Did your .txt burger file which you created complete its upload (turn green) in your history before you ran it. I tried running it on the EU server and the .txt file does not get created. It remains grey. There is still an issue on that Galaxy instance. On the AU server the...
-
Tracey Calvert-Joshua replied to Anne M
@RICHARDOWUSUANSAH Hi Richard, could we kindly ask you to not post any personal information such as your contact details, and to refrain from leaving comments requesting collaborations. This is unfortunately not allowed. Please only leave comments related to the course. Thank you.
-
Galaxy is a gold mine.
-
@DavidWalton were you able to manage on the Australian instance of Galaxy?
Where indicated, it's important to use the instance we recommend, as not all Galaxy instances are created equal. Some may not have certain tools installed.
As it stands, the EU instance of Galaxy have also had storage issues since May, which they are in the process of resolving.
