Installing Vicuna in Biolinux

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Hi everyone,

Today I want to talk about installing Vicuna on Biolinux 8, if you were wondering why that should be something to write about it … well, it has been a hell of a task even for the people helping me. But first thing first what is Vicuna.

From their website (VICUNA) you can read that VICUNA is:

VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage”.

Roughly 3 years ago we had VICUNA installed in our Biolinux system by our IT guy and one of the other PhD students, Gideon Mordecai, found this program very useful for his project and manages to assemble full viral genomes with this piece of software which are published here and here. So we were very happy until the IT left for a new job and long story short I was asked to help with the system that was up and running. This was a great opportunity for me to gain some extra skills and I thought ‘what can go wrong?’ …

I was so wrong…of course something had to go wrong.

After the Christmas holiday, two months after I took over the new system, we got back to the lab to find out that the hardware had failed and we had a technician coming in and installing a new version of Biolinux for us. At first I was happy because we would have  the latest all singing, all dancing, Biolinux 8 installed in our system. Then it also scared the hell out of me, because they told me how expensive the system was and I didn’t want to screw it up. With Biolinux 8 finally installed I spent February and March updating programs and installing the programs needed,  which wasn’t easy since I lacked confidence. But I managed. Since I know that lots of people had struggled to install VICUNA, I left that one for last. I contacted our old IT, and he was so helpful advising me   on mounting the drives but about VICUNA he just couldn’t remember how he managed in the past.

Armed of a good dose of patience I tried to follow the instructions for external users. So first thing first you need NCBI-toolkit v 7.0.0 (but after experience you’ll just need the latest one!). Biolinux has a version of the NCBI tools included but, this is not the one you will need; you will need the ncbi_tools++. How do I know? I have bothered the Biolinux community which, by the way are absolutely amazing if you ever need some help they will be there guiding you and advising you. In this specific case I tried for a very long time to find the library of the tools installed and couldn’t find it … cause it wasn’t there. So I went on and installed a different tool, scared that I was going to kill the system (I shouldn’t have been afraid to mess it up since the system was new and should be working perfectly …. but I was being reminded daily of just how  expensive the guy to install the system was).

I went on and install it in the share directory. Following the instructions from the manual, what I did was:

  1. Download NCBI toolkit from here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT
  2. Untar the folder:
sudo tar –xvf ncbi_cxx--12_0_0.tar.gz
  1. Configure it
sudo ./configure –prefix=/home/share/Programs –with-optimization –with-mt—with-dll
  1. sudo make

This is where all the trouble started with all the possible errors. I’ve tried to install the ncbi_tools++ in the root and then as root and nothing, no way. Frustrated, I decided to ask online. I posted the question here: https://www.biostars.org/p/177810/#177897 and people where trying to help but none of the suggestions were working. And I was losing it (and hours/days of my PhD time). I really was *%$£. I posted for help on twitter and Tim from the UCT eResearch came to help. I know Tim from Cape Town since I am a user of the hex cluster and a registered PhD student of the University of Cape Town. I was very happy when he replied to me and even more since he went above and beyond to help me, following me every step and decoding every single error I was getting. He even installed Biolinux 8 in his machine to replicate it and manages to solve the problem for me.

So after a long rambling here is how to (actually) install VICUNA in Biolinux 8:

Step 1:

Biolinux8 doesn’t have a /opt directory so I created one:

       cd /

       sudo mkdir opt/

Why did I do that? Well, Tim’s advice was that compiling application into /opt will give you more control over it. By the way, ncbi_tools lib takes approximately 50GB of space on your disk, so you want to make sure you have enough space available before you start.

Step 2:

Download and untar the ncbi_tools++

sudo tar –xvf ncbi_cxx--12_0_0.tar.gz

Step 3:

Configure ncbi_tools++. (This is what went wrong previously). The solution was to remove the –with-dll flag and this will make the libraries static instead of dynamic:

cd /opt

As a personal tip: create a specific folder for the libraries, then you’ll know exactly the path.

sudo mkdir ncbi_tools-lib

Then I configured it:

sudo ./configure –prefix=/opt/ncbi_tools-lib –with-optimization

Step 4:

sudo make

sudo make install

NCBI_tools++ are now installed and configured.

Now for the beast which is VICUNA.

Downlad the tar from their website (VICUNA) and untar in the location you desire. I used the Programs folder I had created.

cd VICUNA

bash #it is require to change environment
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/ncbi_tools-lib

cd src

nano Makefile

Here you need to change the path of the library, for me it was  /opt/ncbi_tools-lib. You also need to check the path for g++ and you can do so by typing “which g++” on the terminal and change it if necessary.

sudo make

And VICUNA is up and running ^_^

last step, since ours is a shared system, I needed to change the permission of:

VICUNA_v1.3/bin/vicuna_analysis

But that was it. It really took me a long time to complete this task and took lots of help from amazing people, as we say in Italy “Non e’ stata una passeggiata” (It wasn’t an easy walk) but we’ve made it.

What might make it easier in the future?

Currently if you try to contact the developer you will receive this error:

Delivery to the following recipient failed permanently:
    xiaoyang@broadinstitute.org
Technical details of permanent failure:
We tried to deliver your message, but it was rejected by the server for the recipient domain returnmail.broadinstitute.org by mx2.broadinstitute.org. [69.173.66.189].
The error that the other server returned was:
550 5.1.1 <xiaoyang@broadinstitute.org>: Recipient address rejected: User unknown in local recipient table

And there was no response on research gate. If anyone involved with the original program can change the contact detail on the paper, this might help other users in the future with what is a very useful piece of software.

I really hope this blog post will help you install this software since I know it is very good for viral assembly. A massive thanks to the Biolinux support and Tim Carr from UCT eResearch.

Hope you enjoy and keep in touch,

Cheers

Flavia

 

Plymsef 2016: the conference, my talk and a bit of bioinformatics made simple

This year I was accepted to present at the Plymouth Marine Science and Education Foundation conference (PlyMSEF 2016) held at the Plymouth Marine Laboratory (PML). PlyMSEF is for early career scientists interested in marine research to exchange ideas, present their work and expand their network. If you are keen to see what was shared on social media you can have a look at the hashtag #PlyMSEF2016.

The entire day was dedicated to presentations with various breaks to appreciate the posters. A total of 5 sessions covered various aspects of the marine research: Biogeochemistry, Community Ecology, Climate Change, Hydrodynamics and Modelling and the one in which I presented; Stress and Virology.

All the talks were interesting and showed what projects are running at the moment in Plymouth but also the broad variety of marine research in this area. Professor Stephen de Mora (Chief Executive of PML), Professor Manuel Barange (Director of Science at PML) and Dr Willie Wilson (Director of the Sir Alister Hardy Foundation for Ocean Science) were the 3 keynote speakers of the day, and I cannot lie but I was very keen on the talk about viruses from Dr Willie Wilson  titled: “It’s life Jim, but not as we know it”. It was honestly the best part, and I loved the production of the podcast a war we need as part of his talk.

plymsef

My Contribution at the Conference:

Since the audience was interdisciplinary I decided that my goal for this conference was to make everyone interested and excited about viruses as well as let them leave with a clearer understanding of what sequencing reads and contigs are. Lots of people don’t realize how much we don’t know about viruses, so for the viral section I tried to make sure that everyone understood how diverse viruses are and that are fundamental for the marine environment. Unfortunately not much is known as we are only starting to understand it thanks to new tools and sequencing technology advances. I love this part of my project, so it was very easy to show and share my enthusiasm for marine viruses…but it was slightly more challenging for the bioinformatics.

Lots of my friends get very confused every time I try to explain my work, what they don’t understand is some of the terms such as reads or contig. It was a good opportunity to try to explain it simply. If we want to make changes in our society and ensure the earth is a better place for future generations everyone needs to understand the issues brought up by the scientific community.  I believe that as scientist we should been able to explain our research not just to other scientists but also make it understandable to everyone.

The following idea came to me the night before the conference and I managed to annoy my housemates in the middle of the night testing it out on them. So, what did I came up with? Here it comes:

Let’s start from the beginning…

SLIDE1_bioinformatics-made-simple

DNA is extracted and send for sequencing where  nucleotides are assembled to create fragments called reads. We have now some bigger pieces that will vary from 100 to 300 base pairs (bp) or longer (depending on the technology used) just like the different bits of lego. These will have to go through a quality control… and we will have to remove all the pieces that are not usable:

SLIDE2_bioinformatics-made-simple

Our aim is to have all our reads in the green area (like in the picture above). Meaning you only keep the pieces you need to build your lego model.

We are now ready to run a de novo assembly! So we will create a new assembly (de novo is the Latin term for new)  from scratch using these reads to create longer fragments that will then take the name contigs. My idea was to picture this process like the Tetris game. How does is work:

SLIDE3_bioinformatics-made-simple

Our reads, having passed the quality control, will be used like in the Tetris game and our goal is to create an horizontal line this will be our new complete contig. Of course contigs have various lengths and the process is based on complicated algorithms.

With this idea I really hope that people who have listened to my presentation will next time be able to understand the  terms “reads”, “contigs” and “de novo assembly”  having now a better clue of what these are and hopefully follow the conversation (or at least have the annoying Tetris music stuck in their heads for the rest of the day…or the next time they’ll hear the term de novo assembly).

This is all for now, hope you enjoyed this short blog and please leave some comments on how you liked this explanation!

Cheers

Flavia

 

 

PhD motivation: #IcanfinishmyPhDbecause

I am finally in my third and final year of my PhD program and I know I am not alone in this questioning phase: have I chosen right by starting a PhD? Should I quit and find a job? Should I keep going? I know these are crucial questions for lots of us, so I was wondering when it is time to give up and when you can keep going and finish. I started this blog as a way to communicate and get in touch with scientists and, hopefully, being helpful to people that get lost on bioinformatics issues. I am really trying to keep my blog bioinformatics based, but I think that also posts like this can be very helpful not only for me but also to everyone in my same situation. I started the blog to find a way to communicate with the bioinformatics community and talk about my project while sharing some readings and interesting facts, but one of the many good pieces of advice from my main supervisor was to write and keep writing – even about my PhD experience. So here I am, in a time of struggle, trying to share my point of view, and my doubts about this demanding time of my life. In writing this I hope to get (and hopefully give) some help and support from people around the world who feel and felt the same way during their PhD, while at the same time keeping myself, and others like me, motivated.

My PhD has not been one of the simplest. Lots of unpleasant things happened (you can read it in a previous post here) and I thought that moving back to the UK would have helped me finding technical and personal support to finish my project. Unfortunately, even in Europe I am facing issues that make me consider if I should finish my PhD or not. A very nice friend gave me good advice and asked me if I could answer this apparently simple question: “Why are you doing it?” Well, at first I thought that I always wanted to do research and become a lecturer at some point, but I realised that, on top of everything, I am in love with the bioinformatics (ok, it is a love-hate relationship). When I understood that bioinformatics is my priority, I started thinking that probably I won’t need a PhD to work in this field, as I already have a Masters in bioinformatics and this might be enough to find a position as a bioinformatician or a technician. But, wouldn’t it be better if I also had my PhD? How will a company/institution see my choice not to complete my PhD?

When I started my PhD I was deeply and completely in love with my project; it was everything I always dreamed about and it involved the marine environment, viruses, and bioinformatics. I couldn’t have asked for a better project! Unfortunately, it was fool’s gold and that’s why I am in such a massive struggle, which makes me not a happy person anymore.

Why I don’t feel as motivated as I was at the beginning? I do think it can be a normal process during a PhD program but mainly I feel tired and setting daily goals can be difficult sometimes, especially having to deal with a change in the project during my third year (due to some problems with the sequencing). So for all these reasons I feel like I am failing on every level: apart from a book chapter, I haven’t published a single paper yet, which makes me feel very incompetent. Why should I finish my PhD? Well, for various reasons: I personally feel I have been quite good in building a network of people, researchers and amazing friends. I am also getting independent in my own work and in learning how to ask for help when I feel not capable of doing something. I am learning new skills and despite lack of money I don’t feel I lack in inventiveness managing to meet with the bioinformatics community in South Africa through the CUB meetings in Cape Town.

What would I like to do to help others and myself in staying motivated? I have decided to write a post, of course, and to start a hashtag on twitter: #IcanfinishmyPhDbecause. In this way I hope people will share their goals and this will to help me, and others like me, through the hard time during the PhD. Hopefully it will help us stay motivated and, let’s admit it, sane. Remember: if you and I made it ‘till here, it is definitely possible to make it to the end.

How much do we care about the others? Some reflections on my PhD time, both inside and outside the lab.

The up and downs of a PhD are well known, but the extent of these is different from one person to another. Inconclusive results, personal problems and many other things can affect this “crazy” time of our life. But despite all the drama, I do believe that having the right support from friends, supervisors and colleagues helps to get through this tough time. I have seen so many students crying and shouting, desperate because of lost or finished funding, fights with supervisors, administration problems and all sorts of other troubles.

I am in my third year of PhD and I have to say that it hasn’t been a normal one. As one of my friends pointed out, I have had a particularly weird experience. Lets just say it feels like living in one of those awful movies where tons of bad things happens to the main character and you sit there thinking “come on these things don’t happen in real life”. Well, yes this has been my PhD so far… starting with drowning my laptop in hot tea, losing my luggage after a flight, funding problems, and lately being physically threatened by a housemate and later having my card cloned. Really I am starting to laugh at myself but it’s been quite an experience, all adding up to #PhDlife which for me includes feeling not good enough, feeling like I have not achieved a single thing and feeling that one day both my supervisors realise that I am not worth the time.

What I have realised during this time is that I am growing personally. I am feeling stronger and I would really like to be able to help other people. And this is why I am writing this post. By talking with other students and also postdocs I realised that there are some common points and struggles for all of us, and what I would really like is to open a discussion and have us all reflect on how we think about others as well, and checking if everything is all right. By this I mean we need to truly listen to someone else. Think about the change in their voice, the look in their eyes, pay attention in changes on how they behave. Because we can get the answer “Yes, I am fine.” but there is often hidden meaning behind these words. How often do we talk to a colleague that is not in our office? How well do we know the new intern or the situation of the foreign student in the lab? Have we done something to help that person to integrate and understand their new working environment and, often, their new country?

This is not something I write easily but I have realised that most of us, in various times are too tired or too ashamed or too polite to answer “How are you doing?” truthfully. Or, in my case, I don’t want to bother someone with my trouble (yes, sometimes it does happen that even I don’t want to talk!). I am very lucky in many ways: I have been through quite a rough path in my life, being in and out of hospitals since I was 14, dealing with my Mom’s ill-health (she has been suffering her entire life with various conditions such as spondylitis, arthritis, fibromyalgia to mention few), my Dad has had heart surgery. Finally both my sister and I have had to deal with a positive HLAB-27 test result for autoimmune disease, and both of us are now starting to show our Mom’s pathology. But, as my Mom has always pointed out, we have been lucky. There are people that suffer from worse, and, having seen two of my grandparents dying from excruciating cancers, I can say we are lucky. I feel lucky. And I feel I have to explain that I feel lucky because I have a family that love me, I have a second family in the USA that wait for me to go back and lots of friends, some of which made all the difference in my life. I feel lucky because I know that if something bad happen I have the strength to support myself, and because I have manages through the years to make amazing friends.

So you may ask yourself, “Why is she writing this?” Well it all started after talking with a researcher, someone that I met multiple times during my time in South Africa, and something that he told me really touched me. Last week I spent two days in his lab for some experiments (It was great to be back in the lab and have a break from bioinformatics!) and I was describing my 16 months in South Africa. At one point he told me that he never thought I could have been having such a hard time, because I am always smiling and happy and extroverted. He thought I was surrounded by friends and having such an amazing time. I have been told various times now that I come across as a happy, extroverted person, which for me is quite hilarious since I had to struggle through all high school with massive shyness and being very introverted. But then I remembered reading about comedians; it was an article in some magazine, about Jim Carey, Jim Belushi and Robin Williams, and it was exploring the fact that some of the best comedians suffer from depression. With this I don’t want to say that I am depressed, but that sometimes we underestimate what another person is going through, and that sometimes trying to compensate with too much happiness is actually a request for help.

Regardless of how well prepared you are for these experiences, there is an enormous need for support. A PhD can be a challenging time, especially if you are in a foreign country. Exactly the same day the researcher spoke to me, I found a link on Facebook to an article on how to spot people that suffer from hidden depression (http://www.lifehack.org/articles/lifestyle/8-things-people-with-hidden-depression.html). Because of this I decided to share some thoughts, because I realise that there are so many people that just assume a colleague, friend or student is fine, when they are actually not! When you are away from home, family and long-time friends it can be very overwhelming. Even small things sometimes can be challenging and affect your sanity.

I am glad I have friends that support me, and tolerate my requests for help and talkative dinners when I am in need but I know we are not all the same. Some people are not able to ask for help, and this is why I am writing this post because this wants to be a reminder for me as well. I know we are all super busy, but if we pay a bit more attention to the other person when we talk to someone, then we can actually make a difference and improve someone else’s life, as well as our own.

A Short History of the Discovery of Viruses – Part 1

An amazing report on the history of viruses … have a look at all 4 parts! it is just brilliant

ViroBlogy

The following text may or may not appear in a book of some kind in the future.  However, I thought I may as well share it – both for general education purposes, as well as for comment.  Enjoy!

A Short History of the Discovery of Viruses

While people were aware of diseases of both humans and animals now known to be caused by viruses many hundreds of years ago, the concept of a virus as a distinct entity dates back only to the very late 1800s.  Although the term had been used for many years previously to describe disease agents, the word “virus” comes from a Latin word simply meaning “slimy fluid”.

Porcelain filters and the discovery of viruses

The invention that allowed viruses to be discovered at all was the Chamberland-Pasteur filter.  This was developed in 1884 in Paris by Charles Chamberland

View original post 3,457 more words

Postdoc jobs in microbial bioinformatics in Iddo Friedberg’s lab at Iowa State

Jonathan Eisen's Lab

The Friedberg Lab is recruiting postdoctoral fellows to several newly funded projects. The lab is relocating to Iowa State University in Ames, Iowa as part of a university-wide Big Data initiative. Iowa State is a large research university with world-leading computational resources, and a strong highly collaborative community of bioengineering, bioinformaticians and life science researchers.

The successful candidates will be joining the lab at the College of Veterinary Medicine, Department of Veterinary Microbiology. Areas of interest include: bacterial genome evolution, gene and protein function prediction, microbial genome mining, animal and human microbiome, and biological database analysis.

These are bioinformatics postdoc positions, and the successful applicants would be required to perform research employing computational biology skills.

Requirements: A PhD in microbiology, bioinformatics, or a related field. A strong publication record in peer-reviewed journals. Strong programming skills; strong oral and written communication skills in English; Strong domain knowledge of molecular biology. Salary…

View original post 209 more words

Next generation sequencing (part 1)

Thanks to the development of sequencing technology we are now able to study organisms that we were never able before, due to fact that are not culturable. Can you imagine the great diversity of microorganisms in our world and we know almost nothing about most of them? Well, thanks to the new sequencing technologies we are starting to see a fraction of this diversity, and understand more about these communities. I believe that knowing how these “unknowns” impact the environment will bring us new advantages in protecting endangered environments, understanding nutrient cycles (giving us a new weapon to fight climate change) and also developing new drugs – and why not help on oil spills?!

But, without getting off topic… let’s talk about these new sequencing technologies and why I have decided to blog about it. First of all, this wasn’t an easy post, I’ve kept changing it: more technical, less technical, more journal article like… in the end I decided to take it as a “conversational post”, a start for, hopefully, an open discussion on next generation sequencing (NGS) and how to choose the best one available for a specific project. Which characteristics are you able to compromise for? But mainly: have you considered choosing the technology during the project planning, before starting the sampling? Deciding which technology at the beginning of your project is very important; I have been asked various times now why I have choose Illumina and not 454 or “Aren’t they all the same? You could have choose the cheaper one.” Well… not really, and the main difference is that the technology you choose will depend on the type of analyses you are planning to do, the aim of the project, the sampling and, of course, funding. They all play an important part in the decision.

Nowadays there are so many different sequencing technologies and little research funding, thus it is very important to carefully choose the more advantageous technology for a specific project (please do not choose just because one is cheaper! There are differences in what you will be able to achieve). For example, the other day I was asked what might be the best for a specific project, and I was able to say Illumina but then I couldn’t give much information on the new MiSeq, would that be better? There is lots to consider in order to achieve the best results: it is the same as considering a kit for a DNA extraction: which one of these will give me higher DNA concentrations, the purity of the DNA, affordability and so on.

Different technologies require different amount of DNA and RNA, so you will need to plan your sampling accordingly: will you need to amplify? If not, how much sample would you have to collect to acquire enough DNA for the run? Is it going to be an environmental, human, bacterial, or viral sample? Can you concentrate without altering or biasing the sample? Depending on the type of bioinformatics analyses you want to run on your data, there are differences in the NGS technology, i.e. if you are looking for novel genomes/genes and you are thinking to run de novo assembly you might want to prefer one NGS (for example Illumina) while if you will be working with known genomes you might prefer 454-pyrosequencing and obtain longer sequences. There are tons (unfortunately I mean kind of literally this time) of things to consider; so, how do we choose? Well…as always literature helps, there is no easy way out, but lately I have heard of consulting facilities where a consultant will help you choose the best technology for your project and hopefully deal with quotas from the different companies, this seems a very smart move since it is becoming very difficult to keep up with all the new technologies.

So talking about platforms the major ones at the moment are:

  1. Illumina: http://www.illumina.com
  • Illumina MiSeq
  • Illumina HighSeq
  • Illumina GAIIx
  1. 454: http://www.454.com
  • GS Junior
  • GS FLX
  1. Pacific Biosciences (PacBio): http://www.pacificbiosciences.com
  • PacBio RS II
  1. Life- Technologies -Ion Torrent : http://www.lifetechnologies.com/za/en/home/brands/ion-torrent.html
  • Ion AmpliSeq
  • Ion Proton
  • Ion PGM

All these technologies have different bias which, you will have to consider before choosing the right one for your project, what are you willing to “sacrifice”: false SNPs, uneven coverages, short sequences, homopolymer errors? Which one has the lowest error rate? I found some interesting papers while searching for this information, so here are the links:

Unfortunately I couldn’t find any more recent comparison papers but depending on the field and type of project there are various papers comparing results by using different platforms. I really hope that this post will open up some discussion on how to choose which NGS for various projects and what others have encountered in the path to the planning of a sequencing study.

So … how will you or have you choose the right technology for your project?

Software carpentry bootcamp

And a software bootcamp landed in South Africa… I have to admit I had the best time during this two day course. But let’s start from the top: everyone knows what bootcamps are, well, almost everyone. For someone like me that is not really into gym or fitness, yes that weird place where you are supposed to move on a machine (???) – I am not a gym person so I had to look it up! Anyway various gym programs propose “bootcamps” with different levels and exercises to improve your fitness with a concentration of exercise, so more effect in less time, maybe I should join one… oh well. So, my question was, will a software bootcamp be the same? Running with a laptop and weight lifting a desktop? Mmm not really, but the concept is quite similar, more on the structure level I mean: two intense days on programming and learning new software’s and tools.

At UCT this amazing idea has been brought along with a conference “eResearch Africa” (http://www.eresearch.ac.za or look for the hashtag on twitter: ‪#eResAf14) with one of the goals being to support scientist to optimise their “programming skills” with beginners level introductory programming for research purposes (http://www.eresearch.uct.ac.za/news/learn-code-python-first-african-software-carpentry-bootcamp-eresearch-africa-2014). During two intense but interesting, and let me say fun, days we were instructed by both UCT members and the software carpentry group (http://software-carpentry.org/index.html), on Bash, Git, Github and Python.

Before this course I took various MOOCs through Coursera but I had never heard of the “Software carpentry” so I had a look at their webpage before the course and what they do is very interesting. I have always been interested in science and knew that at some point I had to improve my preparation in programming but before my master in bioinformatics I never took it seriously. Then something weird happened, I fell in love with programming in Python and R, so I was super happy when I managed to get into a PhD project that involved programming & bioinformatics. Mainly what I like about it is how these tools can make the analyses of big data so much easier, and how afterwards you can reproduce the analyses easily and apply the same script in a pipeline and automate the analyses. Don’t get me wrong I am still learning and there is so much I need to learn; I am still trying to improve my skills and is not easy and it takes time but, believe me, it is totally worth it in the long run.

This course for me was a blessing, for the first time after the master in bioinformatics I was able to follow a programming course with real people instead of being sit in front of a computer watching someone from very far talking to me. I do love Coursera and the opportunities they give to really everyone to learn, but it’s good to have someone in “flesh and blood” talking to you where you can ask questions in real time and they can see everyone reaction and interact. One thing that I really appreciate was the use of colour coded post its to check if everyone was following and, after small assignment check when everyone had finished or needed help.

What was good about this course? Well first of all the interactions and the possibility to talk with researchers, students and professors that utilise programming in different environments. It is seriously very interesting to see how we can apply the same tools for different research purposes, listen to how different people troubleshoot and debug and to get new ideas on how to solve code problems or apply to your own research. Secondly I loved the lessons, apart from Bash where I was expecting something more, I had never use git; I knew about it but the various online courses seemed so complicated that I ended up never getting hold of it, while now I am considering asking them for a private account to store my code and move it public once it is ready. As for Python I was both happy and disappointed, I was expecting a bit more for an advance course but at the same time it gave me a bit of confidence on the few things I know how to do.

Courses like this one are super important and also helpful to scientists that have always wanted to learn more about programming or simply how to use new tools for their research but that lack of time, or because often with online courses you ended up getting lost. A first approach, even if condensed into two days can improve the approach to this subject.

Personally I will try to keep up with various courses to get better, while I develop my love-hate relationship with programming.