Great Course if you are interested in dissecting the genome. Galaxy opens up this invisible world and allows even us little people to explore the world once reserved to only Academia.
This was a lot of work and rewarding to complete. The final project was challenging and the forum contributors helped a lot in pointing out good resources or strategies they had used.
by Rhian C•
Save your money and just work through the free Galaxy 101 tutorials on the Galaxy site! I found that the lecturers sometimes used random terminology without ever explaining it (for example, "tags" is another word for sequencing reads, but this is only ever used in RNA-seq methodology, and then only rarely). Also, the final peer reviewed project isn't explained very well and uses tools and methods that aren't even within the scope of the module. Mostly just a waste of time.
by HARSHIT J•
Worst Course ever to be offered by Johns Hopkins and Coursera
by Charles Y•
Thank you Professor James Taylor for this course, and rest in peace! This was a very helpful and challenging course. Galaxy is a very powerful and easily accessible platform, especially considering that it is free to use. There are tons of Tools in Galaxy, and part of the challenge (and frustration!) is figuring out which Tool is appropriate to use (as it is with any Data Science, really). Although the lectures were helpful and informative, you really need to take the time yourself to learn about and read into the different Tools in Galaxy. Do not try to Google answers to the quiz questions or project, or you won't end up learning much by taking the easy way out.
A notable course which introduces you to Galaxy platform. Final project is bit time consuming, but you can finish it.
by Luca B•
The examples and instructions provided in the course are about older versions of Galaxy making it difficult to reproduce the results. What has been taught during the course was not sufficient to pass the assignment, I had to dig around the web to better understand what I was supposed to do.
The Galaxy portal is an easy to use tool that let's you go through the scientific problems easily without having to install every single peace of SW on your machines. Worth knowing it.
In the end, I think that I learned a lot of new things.
by Keivon M•
There is a lot of really essential information in this course. In addition to this, James Taylor is incredibly intelligent and a huge player in genomics. It's a privilege to have access to courses from such an individual. That said, I think a lot of the lectures are a bit without microbiological context. I found myself running through a lot of Galaxy operations and using tools to manipulate genomic data, but without really knowing why. I think it'd be more helpful if we asked a few biological questions, used Galaxy to run some analytics, and then debriefed on how the data can help us answer those questions. Instead you fly through a few tools, generate some data files, and have like a 15 second explanation as to why this might be useful. Personally it just isn't enough to keep me motivated to finish.
The course is well organized, however the program you want to teach is in my opinion very cumbersome, not very useful, and complicated to use. It imposes too many constraints of use and in my opinion overtaken by other tools. I would suggest replacing this course in the future with the explanation of a more modern tool!
by Alessandro B•
I can’t recommend this course, because it presents several flaws:
1) The course is vastly outdated: all the videos refer to tools that in the meantime received major updates or changes completely. For example, the lecture that explains how to use galaxy on the cloud with AWS is currently useless: AWS interface changed a lot in the meantime and even the procedures required to launch galaxy on the cloud are now completely different.
2) The instructions about how to install GALAXY locally are insufficient: it describes only the installation on MacOS (MacOS is no longer fully supported and several tools do not run on MacOS!!). Additionally, it does not explain how to access to fundamental resources (reference genomes) from the local installed Galaxy instance. Without reference genomes, a local installation of galaxy is basically useless.
3) In the video lessons, genomic tools are never fully explained: the instructor provides explanations on how to load the datasets and operate the genomic tools without explaining what each tool option does. This implies that the student will use each tool in each step of the analysis as a “black box”.
4) The final course assignment requires to perform a variant calling analysis. Unfortunately, the course never covered this methodology in any video lesson and the students are left in the complete ignorance. How can a student that has no knowledge of variant calling review other student’s assignments? (reviewing assignments is mandatory to complete the course)
This course was a waste of time, it is not well structured, it is superficial and I STRONGLY recommend everyone to avoid it.
by Julia O•
The cloud computing service with amazon described in the course is not free anymore. I was charged money for using it. The course also took much more time to complete than I wanted to spend. I believe a better design of the project could lead to a more efficient, less frustrating learning experience. Details below.
The usegalaxy server was extremely slow. As shown in the course, I installed an instance of galaxy in the AWS/Amazon Cloud. I was under the impression that this was a free service for the first year. Amazon has changed its interfaces and I could not do the installation as recommended. But I managed to run a few analyses with some workarounds. I did not explicitely terminated the galaxy instance for ~ 6 days. Charges of $280 accumulated.
The course project in week 4 was far beyond what was covered in the lectures. It took me a whole week, spending multiple hours every day. Many dead-end roads coupled with extremely long run times on the galaxy servers resulted in very inefficient learning and many frustrations. Help via the discussion forum was critical to design an analysis pipeline - so thank you Dejan and all contributors for the support.
This is not a course I could easily do part-time: I don’t have time to read the fine print on what is available for free on Amazon, nor do I have time to go through all of the tools on galaxy to find out what would be the best for my analysis.
On the positive side: I think Galaxy is a great tool.
by seyed r m•
I joined the specialization related to this course and I'm quitting it because of this course. My background is in computer science and I was hoping to see its application in Genomics. This course provides walkthroughs of using the Galaxy software with an abundance of domain-specific terms that are not explained in the previous course or this one. After getting through all the quizzes, I succumbed to the final project involving Galaxy. The description of the tasks involved terms I didn't recognize. The forums for that week are inundated with requests by others to mark their project and beginners like me finding it difficult to understand how to do the project. The course feels like a ghost ship. I imagine if you are engaged in this field it is a bit easier, otherwise, avoid it until it is changed for the better!
by Avi B•
Atrocious. The content is insufficient, videos don't nearly try to explain topics, Galaxy is vastly different from what is shown, quizzes don't directly co-relate with the videos, no supplemental material outside of the videos. This course needs serious updating, or should be removed from the specialization. It's painful to go through this course just because I want to finish all the courses in the specialization.
If you want to learn, this course doesn't accomplish that. There's no reasoning explained, you just press this, select that, and get results. But why? Why do we do each step?
I don't even know if the course instructors read this. In the slim chance that this is read, please please PLEASE update this course to be useful.
by Lindsay P•
The course was interesting and the videos were useful, though I think more background information was needed. Also the project was absolute bullshit. We were taught third grade math and asked to do a calculus assignment. To complete this project, I spent over a week googling all the tools used in my workflow and sought additional consultation from those outside of the course. The predicted 2h time frame for the project is completely laughable. Though this course was useful, and I hope to enact the skills I have learned, I hope that in the future this course will be redesigned with more realistic expectations.
by Dhynasah C•
You think this course if straight forward until you get to the project. The project is extremely complicated. It estimates it will take you 2 hours to do. No! It took me over 3 weeks. I finished weeks 1-3 and all of the videos for week 4 in one week and it took me forever to figure out how to do the project. Weeks 1-3 are a waste of your time, they do not explain anything in detail and are super unhelpful for completing the project. You need a lot of prior knowledge to complete the project. I am only continuing with the specialization because I am hoping it will help me get the kind of job I want.
by Hans W•
The lecturer only shortly explains what it is we are trying to analyze. He quickly skips over the biology and tells where to click in Galaxy. Additionally I can understand that frequently you would like to stick to the default values. Every now and then the lecturer changes some parameters without explaining well enough how and why to do so.
The assignment at the end is tough. It is hard to accomplish with only the course material as background. One needs to look for other Galaxy tutorials to successfully complete the assignment.
by Olga L•
I have DS abd CS background and this course was like an ice bucket after "Intro to Genomic Technologies" course. Many genomics unknown terms were just casually mentioned. Videos where mostly about clicking buttons, without not much of WHY.
And the course project is just a pure madness. Has anyone verified that this course make sense end-to-end?
And did I mentioned that pretty much all mentioned tools are deprecated as of March 2020?....
by Yonatan M•
nice introductory course, but materials are not up to date, course project was way too demanding and hard to complete and most of the skills that were needed to complete it werent tought in the course lectures..
by Andrea P R D•
It isn't necessary at all. If you know how to program in Python (what this whole course is focused on) you won't need to use this tool.
by Charles W•
I was able to pass the course course project on my first try, but I think that it might help to provide more background for others with less genomics experience. So, I gave the course 5 stars, but I can see how others might more fairly give the course 4 stars.
Also, while interesting, I wonder if it might have helped to provide a link about how to install Galaxy locally or run on the crowd, without making that a graded section. I used the main Galaxy interface without needing to use those other options. However, I had the impression that running the local instance might help (and I think that can add frustration and/or cost). So, I think not having that as a formal requirement can avoid implying that it might help for the course project.
by Wilson G•
Don't be fooled!! This is how I can get you to know the truth. Instructor does poor in explaining concept behind various tools and analysis. This makes it difficult for beginner level. Instructor assumes students already know about most concepts and jumps straight into how to perform those concept analysis using galaxy.
by Sreenithya R•
This was a great course! For beginners, this will feel very easy in the beginning but there is a lot more to know and understand. One suggestion from me will be to read the manual for every tool you would use in Galaxy. Also, the course lectures need to be updated. Overall, it was a good experience learning Galaxy.
by Angelos K•
The course was of high level and I am glad I learnt a totally new to me tool. I am truly satisfied. If I could propose something to be ameliorated, I would suggest making the videos flow faster .
Thank you for this wonderful course! I am looking forward to starting the next one for the Specialization!
by Ramón Q B•
Me parece que la herramienta Galaxy es bastante completa y que James Taylor hizo un trabajo genial con este curso. He aprendido lo necesario para empezar a trabajar en esta plataforma y el proyecto final te permite desarrollar de manera adecuada todas las competencias aprendidas durante el curso.
by Gouri V•
Very good experience. The lectures seemed to have covered very few topics but I was able to manage. It will be nice to have more information on running galaxy locally and the way tools and genomes can be imported/installed as that is one thing I really struggled with. Overall the course is good.
by Sameer K•
This course is a gateway to bioinformatics applications in genomics. Galaxy has almost every updated tool that is used in NGS analyses. And all that without a need to use command languages. As such, it offers an easy way to handle genomic data. Great course for the beginners.
by Pushpendra S•
It is very nice Course to learn the hands-on dry lab work for Biologists. Its Project assignments in last with review other classmates work made it more valuable. Galaxy local Installation is also very good concept to teach properly.