Many of us work on very exciting projects and in very similar areas of knowledge.
However, what to do when you are "scooped"?
Being "scooped' basically means that at some point you realize that a colleague or another group is doing the same research you are doing !!!
Panic attack, anger, desperation and other symptoms come into existence and your life is ruined, or so you think. I wanted to write this little piece about how to deal with getting "scooped" because after some time of being involved in research it is inevitable that this will happen to you.
Lets, as Jack the ripper used to say, go by a piece at at time, in a numeral fashion, shall we?
1. Keep calm:
This may sound ridiculous but it is essential.
If you are panicking you will see the worse case scenario and will no be able to think straight, so breathe and compose yourself!!!
2. Make sure you are really working on the same questions as your "scooper".
Many times we panic and we don't even read the details of what the "others" of the island are doing. Take your time, and read about what they are doing. They may be using the same system but measuring different things, they may be really far from being at the same point that you are with your system or maybe they are using a completely different approach.
3. Collaborate instead of attack.
We are all scientist and sooner or later we will run into each other, so please don't fall in the cheap and nasty trap of making a competition out of it.
Trying to beat the other group to the publication or talking about how they scooped you at conferences and meetings will only result in poor science and burned bridges.
A nice e mail or phone call may open the door for a broader and richer project. Who knows, maybe you end up doing something the "others" can't or they may have some material you can use. Basically, collaboration may result in more than one publication, sharing of resources and better and more positive research.
4. Innovate:
Well it happens!!!
Is a fact, they did it before you and they published it so now what?
It is time to sit down and explore what other questions can you ask yourself about your system.
It is not the end - it is quite the opposite. Be confident in what you know and what you have learned so far, twist it, and think outside of the box.
The hardest thing to remember is that science should not be a battle of egos and that knowledge will take its course.
I am sure you will be able to survive the "scoop" and that your research will improve when you are forced to take new directions.
Who knows? the "others" may have published it first, but you may be the one who changes the whole game in your field.
Sunday, August 25, 2013
Sunday, July 21, 2013
I want to learn bioinformatics 2
In the order of finishing what we start here is the second part of a previous post I promised some tools and websites to check for people that want to learn some bioinformatics basics.
First lets start on programming languages, to do bioinformatics you don't necessarily need to know programming or scripting but knowing a language will help you to understand some tools you will be using and will differentiate you from a space monkey, that is able to type and follow basic instructions.
What language to learn based in which one is better is a discussion that I will not start, there are many languages you may like or feel more comfortable with a good place to start is codecademy this place has different tools to introduce you to the basic concepts of coding and some languages (Ruby, Python and Java could interest you the most). Their interface is great and is a good starting point.
Each language has their own website with great information and educational tools feel free to visit them and enjoy about the history of Ruby, Python, Java, Perl and others.
Now to get more into biological data related projects Rosalind is a great website that runs on Python with real data sets and projects, go for it!! dare to play and make mistakes.
Now you have a good idea where to start, and I wish you well.
However, wait a moment for some words of wisdom.
Thank you for actually keep reading.
Words of wisdom:
Remember that you are going to analyze biological data, with the last generation sequencing technologies and the accessibility to many different learning tools you may forget the key to nay good scientific research: WHAT IS YOUR QUESTION!!!
Don't run analysis without understanding what questions you will answer and don't separate your data from your system learn about it and understand it as a whole, including variables that may influence it.
There, I hope that last note was not too serious.
Enjoy learning and as my boss says try to "fail better every day" !!
First lets start on programming languages, to do bioinformatics you don't necessarily need to know programming or scripting but knowing a language will help you to understand some tools you will be using and will differentiate you from a space monkey, that is able to type and follow basic instructions.
What language to learn based in which one is better is a discussion that I will not start, there are many languages you may like or feel more comfortable with a good place to start is codecademy this place has different tools to introduce you to the basic concepts of coding and some languages (Ruby, Python and Java could interest you the most). Their interface is great and is a good starting point.
Each language has their own website with great information and educational tools feel free to visit them and enjoy about the history of Ruby, Python, Java, Perl and others.
Now to get more into biological data related projects Rosalind is a great website that runs on Python with real data sets and projects, go for it!! dare to play and make mistakes.
Now you have a good idea where to start, and I wish you well.
However, wait a moment for some words of wisdom.
Thank you for actually keep reading.
Words of wisdom:
Remember that you are going to analyze biological data, with the last generation sequencing technologies and the accessibility to many different learning tools you may forget the key to nay good scientific research: WHAT IS YOUR QUESTION!!!
Don't run analysis without understanding what questions you will answer and don't separate your data from your system learn about it and understand it as a whole, including variables that may influence it.
There, I hope that last note was not too serious.
Enjoy learning and as my boss says try to "fail better every day" !!
Tuesday, July 2, 2013
I want to learn Bioinformatics
I was recently involved in an online discussion about learning bioinformatics and what would be the best first steps to do so.
Is important that we clear the air from the beginning, there is not an specific path or golden way to learn the tools and to master this discipline. From my personal experience it has been a lot of self education and curiosity. But if you ask me what do you absolutely need to embark on this quest, I would have to say that is a very low frustration level. If you get easily frustrated when Windows takes more than two minutes to restart a frozen program you may want to re consider this challenge, you may find yourself trowing your computer across the room surrounded by very frightened co workers.
So if after some self criticism you believe that you have the patience and curiosity that it takes, here is what it has been more or less for me.
I have to say that I do not consider myself a bioinformatician but I can strike some keys, kind of write some scripts and run some analysis on different platforms.
Allow me to lay it down by some numbered and explained points:
1. Learn the basic of UNIX/LINUX command lines: Sorry there is no way around this, you want to be a super geek and you don't know what #$ ls does? Please get it together!!! Almost every tool you will use will be called from a terminal using command lines so the best thing to do is to learn some basic terminal commands and how to move around.
Right now, stop reading this, and try to open a terminal in your computer and play around, look for UNIX (Mac) commands, here you have a good list and nice examples. If you are wondering what is the difference between LINUX and UNIX... there is none!! LINUX is basically the free version of the license dependent UNIX.
2. Play a lot with your terminal: After learning some commands use them!!! open a terminal and try to do basic tasks using some command lines.
Make directories; open files; look into files; move around directories and so on.
This will allow you to get use to the terminal and the idea that things come in like arguments and come out as outputs.
3. Stay updated and read: If you want to work in bioinformatics, read read and read!!! papers, websites, twitter, all sources where bioinformatics tools are used. Ask yourself what tools are they using? What new tools are being proposed? New algorithms ? It doesn't matter if you don't understand all of it, get familiar with what is going on in the field.
I think this is a good beginning for now, in my next post I will give you some online tools for practice with real problems and learning some programming languages.
I hope you start today a nice and fun adventure and enjoy the quest !!!
Is important that we clear the air from the beginning, there is not an specific path or golden way to learn the tools and to master this discipline. From my personal experience it has been a lot of self education and curiosity. But if you ask me what do you absolutely need to embark on this quest, I would have to say that is a very low frustration level. If you get easily frustrated when Windows takes more than two minutes to restart a frozen program you may want to re consider this challenge, you may find yourself trowing your computer across the room surrounded by very frightened co workers.
So if after some self criticism you believe that you have the patience and curiosity that it takes, here is what it has been more or less for me.
I have to say that I do not consider myself a bioinformatician but I can strike some keys, kind of write some scripts and run some analysis on different platforms.
Allow me to lay it down by some numbered and explained points:
1. Learn the basic of UNIX/LINUX command lines: Sorry there is no way around this, you want to be a super geek and you don't know what #$ ls does? Please get it together!!! Almost every tool you will use will be called from a terminal using command lines so the best thing to do is to learn some basic terminal commands and how to move around.
Right now, stop reading this, and try to open a terminal in your computer and play around, look for UNIX (Mac) commands, here you have a good list and nice examples. If you are wondering what is the difference between LINUX and UNIX... there is none!! LINUX is basically the free version of the license dependent UNIX.
2. Play a lot with your terminal: After learning some commands use them!!! open a terminal and try to do basic tasks using some command lines.
Make directories; open files; look into files; move around directories and so on.
This will allow you to get use to the terminal and the idea that things come in like arguments and come out as outputs.
3. Stay updated and read: If you want to work in bioinformatics, read read and read!!! papers, websites, twitter, all sources where bioinformatics tools are used. Ask yourself what tools are they using? What new tools are being proposed? New algorithms ? It doesn't matter if you don't understand all of it, get familiar with what is going on in the field.
I think this is a good beginning for now, in my next post I will give you some online tools for practice with real problems and learning some programming languages.
I hope you start today a nice and fun adventure and enjoy the quest !!!
Thursday, June 6, 2013
RNA extraction first timer!!
I am gettgin reading for my first time extracting RNA.
After long time plating with DNA this seem to be whole different animal already.
Starting with tre prep phase using RNAse away and usgin DEPC water.
I will let you guys now how thigns turn out.
Wish me luck
After long time plating with DNA this seem to be whole different animal already.
Starting with tre prep phase using RNAse away and usgin DEPC water.
I will let you guys now how thigns turn out.
Wish me luck
Monday, July 2, 2012
MacQIIME BLAST installation error
As many microbiologists and other researchers working with high throughput sequencing I've decided to install and work with QIIME (a pipeline of different python scripts that makes our life a little easier).
I have to say beforehand I AM NOT A BIOINFORMATICIAN and I can be very clumsy with this kind of tools.
But I've learned that in microbiology we all have to learns or at least understand basic bioinformatics and programing notions if we want to have some edge and competitive performance.
So I jumped in the adventure of installing MacQiime
First I have to say that the installation in the Mac enviroment is less traumatic than my previuous experience in Ubuntu, I was running a virtual machine and when tried to update QIIME I got frustrating results with the VM and QIIME.
I recomend the Werner lab instructions for MacQIIME installation they are very well writen and fairly easy to follow.
One of the most commons errors in the installation of macqiime seems to be during the installation of BLAST, a tool for taxonomy assignment during the OTU's picking, it seems that a lot of people, like me, fail in the PATH modification step where you basically add the BLAST package to your PATH environment.
So what the heck is the PATH? first let me remind you again that I am not a bioinformatician but a poor computer owner/operator that runs a lot for help to the IT people.
The PATH is basically an "environment" that contains all the variables that are called by the system when programs are run, it connects and allows to call your software files, data and more. For the technological virgin as me the PATH is a long string of "no Idea what the f is this" characters and names that looks like this
-bash: /Users/juangiarrizzo:/Users/juangiarrizzo/blast-2.2.26/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin: No such file or directory
Lets go back to adding Blast to your PATH, in the instructions yo will see that to do so (after placing the BLAST package in your home) you have to modified a file called .profile.
THINGS THAT THEY DONT TELL YOU AND YOU PROBABLY NEED TO KNOW
1) .profile is a file that ir read every time you run your shell (the window where you type your commands)
2) Every time you write something in .profile you are saying to the system to ignore and overwrite what you wrote before
3) And more important you have to restart your shell to make the PATH modifications to work!!! this for the experts is a dah but from us mortals is not!! this measn you have to close and restart the terminal window so the modifications take place
4) Separate any new addings in the PATH with ":" otherwise you are just erasing the previous PATH statement.
Once you do a correct PATH addition for the BLAST package you should be able to locate the executable file "blastall" by typing: $ which blastal
If is not working this may be the causes:
1) You didn't restart the shell after modifying the PATH and adding the BLAST package (see instructions)
2) You overwrote the PATH by obsessively repeating the nano edit step (as I did)
3) Maybe you have the wrong name for the BLAST package in your $PATH, please note if you download the latest package the name is blast-2.2.26 and no blast-2.2.22 as it says in the instructions. Is OK to be a good instructions follower but reading is always advised.
I hope you find this helpful. You can also ask to to the QIIME forum if you run into other more complicated issue, you will find out that there are a lot of helpful and patience people waiting for you.
Cheers!!!
I have to say beforehand I AM NOT A BIOINFORMATICIAN and I can be very clumsy with this kind of tools.
But I've learned that in microbiology we all have to learns or at least understand basic bioinformatics and programing notions if we want to have some edge and competitive performance.
So I jumped in the adventure of installing MacQiime
First I have to say that the installation in the Mac enviroment is less traumatic than my previuous experience in Ubuntu, I was running a virtual machine and when tried to update QIIME I got frustrating results with the VM and QIIME.
I recomend the Werner lab instructions for MacQIIME installation they are very well writen and fairly easy to follow.
One of the most commons errors in the installation of macqiime seems to be during the installation of BLAST, a tool for taxonomy assignment during the OTU's picking, it seems that a lot of people, like me, fail in the PATH modification step where you basically add the BLAST package to your PATH environment.
So what the heck is the PATH? first let me remind you again that I am not a bioinformatician but a poor computer owner/operator that runs a lot for help to the IT people.
The PATH is basically an "environment" that contains all the variables that are called by the system when programs are run, it connects and allows to call your software files, data and more. For the technological virgin as me the PATH is a long string of "no Idea what the f is this" characters and names that looks like this
-bash: /Users/juangiarrizzo:/Users/juangiarrizzo/blast-2.2.26/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin: No such file or directory
Lets go back to adding Blast to your PATH, in the instructions yo will see that to do so (after placing the BLAST package in your home) you have to modified a file called .profile.
THINGS THAT THEY DONT TELL YOU AND YOU PROBABLY NEED TO KNOW
1) .profile is a file that ir read every time you run your shell (the window where you type your commands)
2) Every time you write something in .profile you are saying to the system to ignore and overwrite what you wrote before
3) And more important you have to restart your shell to make the PATH modifications to work!!! this for the experts is a dah but from us mortals is not!! this measn you have to close and restart the terminal window so the modifications take place
4) Separate any new addings in the PATH with ":" otherwise you are just erasing the previous PATH statement.
Once you do a correct PATH addition for the BLAST package you should be able to locate the executable file "blastall" by typing: $ which blastal
If is not working this may be the causes:
1) You didn't restart the shell after modifying the PATH and adding the BLAST package (see instructions)
2) You overwrote the PATH by obsessively repeating the nano edit step (as I did)
3) Maybe you have the wrong name for the BLAST package in your $PATH, please note if you download the latest package the name is blast-2.2.26 and no blast-2.2.22 as it says in the instructions. Is OK to be a good instructions follower but reading is always advised.
I hope you find this helpful. You can also ask to to the QIIME forum if you run into other more complicated issue, you will find out that there are a lot of helpful and patience people waiting for you.
Cheers!!!
Friday, June 29, 2012
Greetings and introduction
There are several reasons to write a blog probably the best one is to share experiences and expertise that you may think can help others.
But, in all honesty I think the more truthful is that we want to in somehow, remain and resonate in the web and feel a sort of feedback about opinions and experiences. After all, the whole idea is to feel the illusion of connection and contribute in a humble way to our field of expertise.
So what is this blog about?
I am a Postdoctoral Researcher in environmental microbiology area, with more than ten years experience in academia. Additionally, I have worked in different professional settings outside academia including film production and import/export. I have accumulated experiences and learned about not only techniques but also about horizontal management, problem solution and negotiation.
I hope, this blog becomes just not only a personal diary but also a good reference for other scientist fellows and for those that like me share the experience of being a scientific with an entrepreneurial soul.
But, in all honesty I think the more truthful is that we want to in somehow, remain and resonate in the web and feel a sort of feedback about opinions and experiences. After all, the whole idea is to feel the illusion of connection and contribute in a humble way to our field of expertise.
So what is this blog about?
I am a Postdoctoral Researcher in environmental microbiology area, with more than ten years experience in academia. Additionally, I have worked in different professional settings outside academia including film production and import/export. I have accumulated experiences and learned about not only techniques but also about horizontal management, problem solution and negotiation.
I hope, this blog becomes just not only a personal diary but also a good reference for other scientist fellows and for those that like me share the experience of being a scientific with an entrepreneurial soul.
Subscribe to:
Posts (Atom)