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Volver a Biology Meets Programming: Bioinformatics for Beginners

Opiniones y comentarios de aprendices correspondientes a Biology Meets Programming: Bioinformatics for Beginners por parte de Universidad de California en San Diego

4.4
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950 calificaciones
271 revisiones

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Are you interested in learning how to program (in Python) within a scientific setting? This course will cover algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms in Python. It offers a gently-paced introduction to our Bioinformatics Specialization (https://www.coursera.org/specializations/bioinformatics), preparing learners to take the first course in the Specialization, "Finding Hidden Messages in DNA" (https://www.coursera.org/learn/dna-analysis). Each of the four weeks in the course will consist of two required components. First, an interactive textbook provides Python programming challenges that arise from real biological problems. If you haven't programmed in Python before, not to worry! We provide "Just-in-Time" exercises from the Codecademy Python track (https://www.codecademy.com/learn/python). And each page in our interactive textbook has its own discussion forum, where you can interact with other learners. Second, each week will culminate in a summary quiz. Lecture videos are also provided that accompany the material, but these videos are optional....

Principales revisiones

DL

Apr 18, 2016

I give this course 5 star because I did Bioinformatics I and I totally enjoy it.\n\nThis is where programming can be fun, and practical, and you'll learn some basic biology too.\n\nWhat's not to love?

HL

Aug 16, 2017

I learned a lot from this difficult and time-consuming course! It covers biological concepts using Python. It made learning Python more interesting for me, since I have always loved biology.

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1 - 25 de 268 revisiones para Biology Meets Programming: Bioinformatics for Beginners

por Kerry

Jan 15, 2019

This is a poor course for Python beginners. There are two things going on here -- CodeAcademy, which has a nicely thought out, clear explanation of basic Python programming. Then there is STEPTIK--the big problem is that the very basic programming instruction in CodeAcademy does provide adequate background to successfully solve the problems in STEPTIK. The STEPTIK section should build on/fill in the gap between what we learned in Python and we need to still learn to complete the problems. Many of the solutions provided in the solutions forum use coding that was not introduced to us in CodeAcademy.

This course may work for computer programmers who want to explore Bioinformatics. After trying twice to complete Week 1, I finally gave up. What's the point if I have to copy solutions from the Solutions forum (that I don't understand) to proceed? I'm glad I did not purchase the course before I tried out Week 1.

por Sophie A

Feb 07, 2019

Not at all for beginners. A coding background is necessary to make any sense of the material.

por Muhammad A

Jul 31, 2019

It's too difficult as a beginner and introductory course, especially Weeks 3 and 4.

por Puneet K

Apr 11, 2019

in between the course the continuity breaks and also it jumps to a sudden high level

por Kaushal K K

Jun 30, 2018

This course is rather fun to take!! It slowly builds your knowledge base in Python (mostly through CodeAcademy exercises), while at the same time giving biologically-relevant problems to solve so that you get some practice in applying what you learnt in a real-world context. I would especially recommend it to Life Science-trained people who want to learn how to program in Python, but find themselves put off by the fact that most of the practice problems out there are not very relevant to their field, such as constructing irrelevant programs, for example. In this case, such people are will find themselves at home in the problems given in this course. The familiarity of the context in which the problems exist proves to be quite motivating, and makes the task of trying to find the solution using programming very rewarding. Most of the problems revolve around finding different kinds of patterns in DNA strings, such as finding frequent kmers, finding motifs, etc. But don't worry, you aren't just finding them for the sake of finding them, there is a very real biological question used to frame these pattern-finding problems, which prevents this course from being dry.Just take note though: you must try and complete at least a few units CodeAcademy Python track BEFORE starting the course, instead of starting DURING the course as expected. This is because during the first few days of the course, it can be quite distracting to constantly jump between the course material and CodeAcademy, which might break your link and cause you to lose interest in the problem you are currently trying to solve. Solve some CodeAcademy units first, and then tackle the problem in a more continuous manner.

por Carlos M

Jan 24, 2019

excellent introduction, which was at an appropriate level for my experience (lots of programming in languages other than python, and just a cursory understanding of genomics).

por Nihar S

Mar 14, 2019

It was definitely interesting and quite challenging. But in my opinion it is a little hard for beginners. I am glad I did it though. Looking forward to the specialization.

por Pablo G N

Apr 01, 2018

Definitely, it is not an introductory course to programming in Python. Exercises that have a 15-minute resolution time estimate, for someone who is programming for the first time, can take several days. The comments section of each exercise is full of people who are unable to solve the exercises because the basics of programming are not well explained.

por Joao M

Oct 16, 2019

Great great course ! Many thanks for those who made it possible, as i learned a lot. I am a seasoned programmer in manny languages so i have learnt both Pyhon and genetics. Very happy !

por Om P

Jul 02, 2019

Very informative, easy to follow, wonderful lessons, I could go on and on. This course really helped open up my mind to this wonderful field at the intersection of bio and comp sci.

por John B M

Sep 03, 2019

Warning: Unless you are experienced with python scripting, this course will NOT be quickly finished. Exercises are solved by typing (or pasting) in your python functions. The website supplies the input variables and runs any additional functions (such as looping your algorithm 1000 times). Often you cannot see the input variables or the additional functions applied, which can make troubleshooting difficult. Typically my first few submissions would be wrong; the code worked on my laptop but not on the website. It was difficult to track down the incompatibility or my error, since I did not know what the website was trying to do.

There are four parts. Part 1 is simple and easy, typically 1-3 functions per exercise. Part 2 starts to combine more functions towards the end. Part 3 and part 4 took me probably about 8-10 hours of work each, with the reported aggregate success rates on several exercises between 10-13%. It wasn't uncommon for people to comment they'd spent days on a single exercise (there are about 10-15 exercises per part). Occassionally someone will post answers to the exercises in the comments, but this is rare. Usually, you're on your own until you figure it out. You can read ahead, but you get no points until you go back and complete missing exercises. Once you complete an exercise, a solution forum opens where you can read how others did it much better than you.

Nevertheless, if you google (constantly!), spend many hours, and ask questions in various fora on the internet, you'll eventually find a solution. Along the way, you should be ready to tear out your hair over your code being repeatedly rejected as wrong. Apparently this latter ritual is also a measure of your quality in bioinformatics, since everyone who works in this field must be prepared to endure the grief of inexplicably failing code, persisting until a solution is found. So the frustration is supposedly part of the learning process.

Ultimately, this is how you will learn what your code is doing. You dive into it with pdb and check everything at every step until you understand the code. It can take a few minutes to an hour, but usually you do this anyways in order to troubleshoot.

Outside of the step-by-step function of your code, the broad goals of what you're doing, the aim of your algorithms and the biology, are mostly well explained. The text frequently invites you to stop and think, which for me meant stop and read others' comments, since some people are very good and post some enlightening commentary, which became part of my education. Every part has a couple optional excursions where you're debriefed on historical or related knowledge, which were actually surpisingly fun to go through. It was nice to read short, interesting sections without the pressure of a looming exercise to cap it off.

There is however no pressure. The exercises are not on a deadline. The quizzes can be repeatedly attempted until you have a 100%, with about half the questions never changing, and the other half typically only changing the numbers. Can't comment on the videos as I never watched a single one, just did the Stepik exercise program.

This course is marketed for beginners, but there's a big caveat with that (hence my 4 stars for that deception).

I began with a warning, so I'll end with a reminder of that warning:

Constructing your coding is not well explained. You're given a goal that's usually clear, but the "how to reach that goal via python" is almost always entirely up to your programming intuition. Your biology knowledge won't help you at this in any way. If you suck at programming / never scripted before, and you're looking to have your hand held through python, then either don't do this course, or maybe make sure you have the recommended codeacademy accompanying course for Python. I didn't do the codeacademy course, so I can't vouch for that, but maybe it will help. I know from others' comments on the exercises and my own experience that this can take over 10 hours for either part 3 or part 4 if you don't know what you're doing, and at times, specifically regarding errors in your code, leave you at a frustratingly complete loss for how to proceed, where you're on your own to figure out how to get your code working.

por Zhenan L

Aug 20, 2019

Figure???Figure??? 80% figure were not working??????

por Adam R

Jun 02, 2020

Exciting and very informative! I'm a high school student who loves biology and Computer science, and learning these two at the same time was such a great experience. Even though it says that it's a "beginner course", it definitely is a challenging course which makes it even more exciting! I thank all the people who worked hard to put this course together and cheers to the people who were able to finish this course with me!

por Kshitij S

Dec 23, 2018

The course was fairly interesting and I had a lot of fun in completing it. The only problem I had with the course was with its python aspect. Apart from that, it was amazing!

por Aquil

Jan 14, 2019

I really enjoyed the class, however, I have two complaints/recommendations.

1. Much of the content seems geared towards biologist/life science professionals who have a strong grasp on the concepts being presented. I am a software developer with little background in the life sciences, much of what was discussed as it relates to biological processes was new to me. It would have been nice to have had a companion document for the biology side of the course, similar to the Python programming companion.

2. Successfully completing work in Week 4 depends on successfully completing the "GreedyMotifSearch", I didn't search the forum or FAQ too much, but providing more visible support for people who get the correct answer, but exceed the time limit might be useful. I was able to easily identify my problem using a line profiler, but those new to Python may not know "Best Practices" for optimizing code.

Anyway, that's it. Thanks.

por Clara B

Oct 17, 2017

There are better ways to learn python for bioinformatics than codecademy. I was highly disappointed by this course.

por Ella P Z

Apr 04, 2018

Not for beginners, and requires too much time (even more than it says)

por Jonathan G

May 19, 2016

Frustrating as hell. Too much math and computer coding.

por C.C.

Mar 04, 2018

not friendly for noob

por Danny W

Jun 09, 2016

An excellent course that is a great opportunity for anyone interested in bioinformatics, no previous experience is necessary but either a biological, mathematical or computing background will give you advantages in certain areas. Being a biologist I struggled at first and many of you may do the same but stick with it, work hard on it and you will be rewarded and it is incredibly satisfying.

Due to the practical coding nature of the course, each week can take up a lot of you time. Best if you have a few weeks free (e.g. a graduate student like me) so you can spend a few whole days of it but could be done before/after work if you are motivated and plug away at it each day - just something to keep in mind though, don't expect a light easy 1 hour a week course, it is intensive but in a good way. It can get frustrating, you will want to give up time and time again....but stick at it and you will have a shiny new Coursera certificate and a wealth of programming knowledge under your belt once you finish!

A massive two thumbs up for this course, one of the best ones out there that gives you real worthwhile skills that employers and academia want. Thanks to all the course staff for a great experience!

por Maria L

Aug 30, 2019

Coming from a Computer Science background this course is very interesting and relatable. The coding part is pretty easy, so if you are familiar with any programming language, I think the programming part will be easy for you. I definitely recommend this course to anyone familiar with programming, who is also interested in the bioengineering aspect!

That being said, I like the idea of the course, but I encountered some issues with stepik's online classes/texts.. Their servers seem to be down so I am not even able to complete the interactive text part at the time I want (I keep getting 500).. I was expecting something more reliable especially since this is not free .. But again the idea is cool just wish there were no down times

por Yee L T

Apr 16, 2020

It is not an easy course. I mean given that if you aren't as fast a learner as some others, you might take alot more time to try to understand the concepts both of the programming and why you are using certain methods to solve a certain biological problem. I had to also rely on other sources online to help me understand some parts of the python programming and to reinforce some concepts but I think this is given as I really have no clue! It is a huge undertaking for these course instructors to try to create a short enough yet comprehensive program and I think they have done exceptionally well especially with the abundant practice (coding) material (yes you have to work hard on these, but it does pay off). Thank you so much!

por 孔令根

Sep 13, 2017

My major is biotechnology, I have learnt C program before and I quite enjoy programming, but my major courses have nearly nothing to do with programming, which made me worried about the waste of my knowledge. But now, I feel so excited and refreshed, cause I have learnt how to connect both subjects! And I want to say that this course is very clear with beautiful illustrations and has lots of expansion which can lead us to continue further study, though I have a problem that I can't watch the teaching video, what a pity~

And I'll definitely continue the following course: Bioinformatics Specialization!!!

por Philipp M

Aug 10, 2017

I really enjoyed this course! That's why I will definitely dive into the Bioinformatics Specialization. The presented material is well explained and the coding challenges are increasingly demanding and motivationally designed. Furthermore the instructors are always helpful pointing in the right direction without revealing too much.

Maybe a little advice: If you are completely new to programming or biology (or perhaps both) be prepaed to spend more than 4 h/week because you'll propably need more training time.

por Matchy L

Jan 13, 2019

The course provides some meaningful questions in biological context (rather than abstact excercises in some textbooks) for you to solve. It is really fulfilling when you put what you learnt into use and made improvements on your code to solve the questions better. The exercises are actually challenging for programming beginners. But if you persist, upon completion of this course you will find youself equipped with some solid knowledge on bioinformatics, which will definitely benefit your future career.