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@biotician-blog
A personal blog with public content.
It have been a long time that I did not publish here, and this is mainly because I rebased my blog at http://ssh.bio. I will write new posts at ssh.bio and publish a link here biotician but well, studies, other projects, firends to see...
I changed the name because twitter.com/biotician was not free. I’m now sshbio everywhere on the web.
My dotfiles, but also a bit more.
How much time do we spend writing text?
I wrote thoughts about the importance of text editors and reviewed some of them.
DNA Chaos Game Representation (CGR) are visual, often colorful ways to represent some DNA sequence (proteins too), which size can vary between a few nucleotides and the full genome of a human.
It is a grid on which are placed words : small sequences from the genome (like ACTGGCGTTC). For each position of the plot, there is a corresponding word, and for each word, there is a corresponding position on the grid.
As an example, the word AAAAA may be on the bottom left hand corner, and the word CCCCA on the middle of the left edge. For more details of how it is built, this helps.
This approach considers genome as a book, with parts of the whole sequence as words, and each four nucleotides as its alphabet, then give a synthetic overview of the words it uses: the brighter a region is, the most often the corresponding words appear in the genome.
In practice, two CGR for two genomes of the same species will be highly similar, whereas two genomes from two very different species will be more likely to differ. As an example, the mouse (Mus musculus) and the human androgen receptor on the figures above are (or comes from) closely related species, and both have these dark empty regions.
What is interesting to notice is that sometimes, unrelated species can reveal some similarities, like human androgen receptor and the Anaerolinea thermophila (bacteria). The latter has the same empty regions as the human.
Since bacterias have few DNA that doesn’t correspond to some protein, maybe the similarities could come from the fact that these sequences both mostly correspond to proteins. For the whole genome of another eukaryote (that may have regions not corresponding to proteins), like the yeast (Debaryomyces hansenii) the CGR is more homogeneous.
These images comes from this website. And you can try to produce your own CGR, by choosing a word length, pasting some sequence, and submit. And the G-language Project made zoomable CGRs using the Google Map engine.
Hero.Coli | A synthetic biology game.
This page DO melt together:
Commercial presentations for super-modern software (scrolling animations),
Scientific paper (”Weiss et al., 1999”...)
Microbiology book (with diagrams),
Programming API reference,
Online store game description,
An upcoming big event homepage,
And a smartphone app !
It is a computer game that allow anyone to deal with synthetic biology and genetic manipulations without facing any “risks to the environment, biodiversity, biosecurity, ethics, and health” concerns.
It is based on software standard from some foundation-laboratory-media-network-company-software-conference-academy-community-standard combo, and invite the player to become a synthetic biologist.
You can try it online here: http://herocoli.com/lates
Higher resolution of my last post
This may be among the first bioinformatics fan-art: Enjoy!
Science fiction!
Unfortunately, there isn’t yet a widespread culture specific to bioinformaticians. But this allow anyone to imagine it its own way.
This may be among the first bioinformatics fan-art: Enjoy!
This is a terminal window on running a linux console. This terminal is called cool-retro-term and brings these cool-retro-effects.
It runs real software: Vim, a text editor, and everything else is ASCII art representing random laboratory results.
Having fun with microarrrays!
These are things you can print, not like regular ing of a sheet of paper, but quite!
Two videos to understand how this have been done:
What is a microarray and what ist is usefull to:
How are microarray printed (that goes fast!):
What an elaborated machinery!
Ribosomes (green and yellow) are the enzymes that synthesize proteins.
The RNA (black strand passing through yellow unit) contains the genetic code that tRNA recognise (dark blue). The tRNA bring the correct amino acid to form the protein (growing black chain at the top).
This will later be inserted into the cell membrane (black stripe shown later in the gif), thanks to a translocon (light blue on the membrane).
In many respects, we understand the structure of the universe better than the workings of living cells.
Bruce Albert, author of Molecular Biology of the Cell
A new laser instrument developed for the International Space Station is expected to generate incredible 3D maps of Earth's forests.
We can already mesure the amount of CO2 present on each corner of the atmosphere, but imagine we could quite exactly mesure the carbon stocked on the trees of the whole earth forests.
These are precious datas for many scientific domains, given the current ecological situation. And that's what the NASA is working on, and may deploy soon in the International Scientific Station (ISS).
Bonus: You can see the ISS live from the space here!
The good books
This is a list of the books I use and that were advised to me during my biology class at university, of the books I know to be good, a lists of books lists... This is a list of good biology and bioinformatics books.
It's going to be updated, then don't hesitate to bookmark this page for latter new books!
These books selection is the one I use, and I intented to select the most widely spread with minimal overlapping chapters so that all of these books to be hold together
Biology books
Biology - Campbell
If you've never studied biology, or if you want a wide background on many domain of biology, this book will give you an introduction to life and biology.
Amazon - Google Play
Molecular Biology of the Cell - Alberts
This single book icontains most of the essential knowledge for a bachelor degree! It's a basis many time advised by my teachers.
Amazon (sixth edition) - Google Play
Principles of biochemistry - Lehninger
A widely recognised biochemistr ybook, that havethe advantage to don't contain much cell biology, then which perfectly accompagnate the previous book. This book doesn't include plants-specific biochemistry.
Amazon
Biochemistry - Stryer
This is a great compromise between both biochemistry and cell biology, and may be well suited if you don't need such biology background.
Amazon - Google Play
Plant Biochemistry - Heldt
This is the missing chapters of the Lehninger's biochemistry about plants.
Amazon - Google Play
Genes XI - Lewin
This book is a complete introduction to genetics and molecular biology for the genome working.
Amazon
Chemistry books
Physical Chemistry for the Life Sciences - Atkins
From the author of Physical Chemistry: Thermodynamics, Structure, and Change (the reference in its domain, amazon), it's the simplified version for biologists, containing all of the physical aspects of chemistry.
Amazon
Organic chemistry as a second language - Klein First semester topics Second semester topics
Organic chemistry is the chemistry of carbon-rich compounds: most of the compounds in biology. This is the best explained chemistry book I've found, and it covvers the theory of mosts of the reaction I'll ever encounter in biochemistry. He also reedited both book into a single one, more focused on exercises and practice.
Amazon (book 1, book 2) - Google Play (book 1)
Books lists
Bioinformatics
Amazon bestsellers
Bioinformatics.org (wiki) book list
International Society for Computational Biology (community) book list
goodreads list
What if the technology that is about to replace the current computers wasn’t even faster to solve a simple Sudoku? The quantum computers are often cited as being the future of the computers, but they only are faster for specifying problems, the same kind of problems for which bioinformatics need more performance.
Quantum physics, once it have been introduced, disturbed minds for two reason: it came like a contradiction of many many physics concepts, and it have mind breaking concepts, like things that doesn’t have determined shape or states, or phenomenon that actually change their rules once you try to measure them. These are the physical properties that quantum computers exploit to perform new kind of calculations, giving as a result a set of probability instead of determined answer.
Even if it seem weird, this is very important for biology: life is composed of complex macromolecules for which an infinity of possible form are possible, and a wide part of bioinformatics consists on predicting and suggesting the shape, composition and interactions of these molecules such as DNA or proteins.
To get the result of some of these problems, we would currently have to wait several century to get the exact answer: we are constraint to use estimations to get some answer before it’s own death! With the birth of quantum computers, the calculation time for such problems will suddenly become accessible, giving accurate estimated answer in significantly lower amount of time.
A few years ago, some answers requiring heavy calculations was considered as inaccessible to the human, because of the hundreds of years the calculations would need, even if more efficient computers would be invented (following the Moore’s law). The birth quantum computers is pushing the limits of which answer are accessible for us to know. Are we really ready to receive them?
This is the central unit of the D-Wave quantum computer owned by both Google and NASA to experiment it’s performance.
When biology says "Come on with me!"
Since the natural science has its basis knowledge, it began to subdivide in many domains, with everyday more specialized scientists, deepening the many study fields, leading to a very pointy and specialized research world. Nowadays, biology problems are getting complex, sometimes even surpassing the domain they belong, requiring a interdisciplinary approach to be solved.
Here comes integrative biology: it aims to study biology problems using biology in association many other fields, including informatics, to understand complex biology cases.
Integrative biology, it's when a molecular biologist realizes that cells lives together forming tissues, it's when a physicist discovers the blood pressure phenomenon, it's when an ecologist discovers the past of the species... And it's also when a biologist use computer tools to analyse its experiments results.
I’ve finished my internship report, and like a scientist, I published it. And like a scientist, it is on a university website. And like a scientist, you can read it, and then you will figure that I’m actually not a scientist at all for now!
The chance to try
I finished my internship at the university of Angers, and I enjoyed how catchy it was. I had the chance to try programming for biology (Python, PHP, JavaScript programing languages), and even contribute to some projects. Here is a list of everything I have done thank to the biologist and informatician/statistician that squared my internship: I contributed to the enhancement of the protein database of the university, the LEAPdb and SHSPdb, which are a selection of specific proteins from global protein databases.
Adding the interface from the Multalin tool to both databases. This tool is a multiple alignment software, made to highlight similarities and differences of protein sequences. You can try it by pushing the Start Multalin! button.
The other thing I did witht the databases is a try to bring more information from other databases to complete the SHSPdb: adding 3D scan of each protein, but I hadn’t time enough to finish it.
I also had a few time to start very small personal projects. You can see them at the GitHub page that I created for this occasion. But be warned, it may contain some biology oriented source code!
Fold It is a game that help researchers to find how proteins get folded.
If computers can make more calculation than humans at the same time, they lack ways to interpret complex problems such as proteins folding. But the humans can !
Predict the present
Do you think that molecular biology needs most advanced physics knowledge ?
When proteins are synthesized, many force fields are applied between every atoms of the proteins, making the amino acid chain moving until a stable balance between those physics properties is reached.
The number of folding possibilities is greater than the number of atoms in the universe, but the proteins quite always find the energy-optimal form, in less than a microsecond.
To predict the way a protein will fold based on its composition (in amino acids), there would be so much calculation that we wouldn't be sure to retrieve the result before the end of humanity.
An alternative solution is to "scan" the already folded protein (by cristallography, magnetic resonance...) to reconstitute a 3D image of it, but then, it's not possible to predict what will happen if certain proteins are modified by genetics disease; and in the organism, the proteins are always changing. Moreover, some proteins keep in a unshaped, floating structure, and only fold themselves during the interaction.
Only approximations are currently performed, based on statistics trying to get the most relevant result in a reasonable time (heuristic approach), without actually knowing all of the physics interaction that occurs on the proteins.