SolEol: Automatic search and download of movie subtitles

19/05/2012 à 13:35 - No comments

     I recently found a very interesting tool: SolEol. This tool will help you in finding subtitles for your movies. You simply need to "Drag and Drop" your movie file in the appropriate window in SolEol and it will search the internet for the subtitles in any language. This tool uses the subtitles from the very good OpenSubtitles project.
     In the Menu, you can define your preferred subtitles languages, choose the option "Rename Subtitles as Movie" to show directly the subtitles when the movie starts and also save your username and password if you have an OpenSubtitles account.
     I cannot say more about this tool as the communication (on their Twitter and in some parts of the website) is mostly in Spanish but the project seems very active and new features such as video format conversion will be coming soon.

     SolEol is available for Linux, Windows, Mac and even PPC Mac and is under Creative Commons Licence.

Tags : Software

hubiC: your secure hub in the cloud

14/05/2012 à 04:40 - No comments

     OVH is a french hosting and internet solution provider. Actually this blog is hosted by OVH. Few months ago, OVH released their new project hubiC (hub in the Cloud). This project is similar to DropBox, iCloud or very recently Google Drive. I didn't tried these cloud storing services thus I cannot compare them, but I really like hubiC.
     With hubiC you have 25 Go of storage place for free. If you want more space you can choose other options: 9.90 €/year for 100 Go and 69.90 €/year for unlimited space. You can save everything you want and access it from everywhere with an internet access. To create an account you simply need to register with a username and password. Different tools exist for accessing your hubiC storage place from almost all the mobile and desktop operating systems.
     I recently tried the iPad version of hubiC. After your login you access your folders, you can create or delete folders from this app. The iPad version contains an image and pdf readers to see your files contents.
     I also like the secure part of hubiC. Nobody can access or check your files, you are the only owner of all the data you have in your hubiC. You can upload any type of file (pdf, doc, jpg, wav...) up to 10Go. A sharing option is available on hubiC: by simply clicking the “share” button, you obtain a link that you can send to people you want to give access to a given file or folder in your hubiC. For now, most of the hubiC tools are in beta but the project is growing very fast and new options such as online file editing or private sharing will be added soon.
     If you want to give a try, you can have a look here (only in French).

Tags : Software

How to unlock any jailbroken iPhone using SAM

26/04/2012 à 13:55 - No comments

UPDATE: This method is not working anymore, Apple has patched their activation servers.

     If you have a jailbroken iPhone and you are stuck with the simlock, read carefully the following howto. SAM (Subscriber Artificial Module) is a tool available on Cydia which unlocks any iPhone in any Baseband. To do so SAM is using the original information of the official carrier to allow the activation of the iPhone in iTunes. Here is a very easy tutorial to unlock your iPhone:

• 1- Installing SAM: to install SAM, go to Cydia and “Manage” in the lower part of the screen.
  
  • Go to “Sources”, press “Edit” and add the following source: http://repo.bingner.com
  • You should see Cydia installing some packages.
  • Press on repo.bingner.com and install the SAM package.
• 2- Put the original SIM card in the iPhone, the one to whom it is blocked.
  
  • Open SAM.
  • Go to Utilities and press “De-activate iPhone”.
  • Go back to SAM main screen and press “General Info”, you should see the state of the iPhone as “unactivated”.
  • Copy the IMSI number under "SIM Details" to the clipboard, press this number, select it and copy, we need this number for later.
• 3- Put the other SIM card, the one you want to unlock the iPhone for.
  
  • On SAM select method and choose “Select by Country and Carrier”.
  • Choose the country and the Carrier for whom the iPhone is locked (the one of your first SIM card), and also the ID. If they are multiple ID, you will have to try each.
  • Go to “General Information”, and paste the IMSI number under SAM menu.
• 4- Attempting activation
  
  • Go back to the main menu and “Utilities” and press “Attempt Activation”, the iPhone should respring (black screen for a few seconds).
  • After this step you have to disable SAM by turning off “Enabled”.
• 5- Connect to iTunes
  
  • Now, you have to connect the iPhone to iTunes and get a popup error message.
  • If you don't have the popup error message but just iTunes saying “the SIM is not valide”, un-plug and re-plug the iPhone until you get the popup error.
  • Click Ok, and reconnect your iPhone to iTunes.

     VOILA, you have an unlocked iPhone. The only point you have to keep in mind, is that the iPhone will only work with the new SIM and is not unlocked for all carriers. You will have to repeat the previous steps to activate other SIM cards. Finally, I would like to thank Sam Bingner for this great job.

     Good luck and let me know if you managed to unlock your iPhones...

Tags : HowTo

Alternative splicing in cells

15/04/2012 à 14:31 - No comments

     Genes and proteins are very important elements for the life. They are the sine qua non for all the processes taking place in the organism such as development, growth, respiration, immune system, etc.
     All the genes and proteins are defined in the DNA (DesoxyriboNucleic Acid) molecule which contains our genetic information and is composed by a succession of nucleic acid sequences named introns and exons. This DNA is not used as it is but is first transcribed to a pre-mRNA (RiboNucleic Acid) molecule and then translated to a gene encoding different proteins. The splicing is taking place between the transcription and the translation processes. The role of the splicing mechanism is to remove the introns from the pre-mRNA and produce an efficient mRNA molecule which will be translated to a protein. This removal is possible with the formation of a complex of proteins named spliceosome. The spliceosome will link two following exons and remove the inron between them.
     The removal of introns can vary from time to time for the same gene. It is not always the same introns that are removed and the same exons that are kept, thus we obtain different proteins from the same gene. This process is called alternative splicing.
     Alternative splicing affects more than 90 % of protein coding genes in Human. With the production of different proteins from the same gene, the functional role of the gene is increased. We can have different proteins with similar or completely opposite functions for the same gene. Some diseases are also alternative splicing related such as: a type of breast cancer, spinal muscular atrophy, cystic fibrosis, etc. Alternative splicing plays an important role in the definition of the sex in Drosophila :) and other important mechanisms in the cell in many different organisms.
     Different types of alternative splicing exist. See also the following picture where the exons are represented in blue and the introns in yellow.

• skipped exons or cassette exons: an exon is either retained or removed.
• mutually exclusive exons: one of two exons is retained in the final protein, but not both.
• intron retention: the non-removal of an intron.
• alternative acceptor and donor sites: variable start or end position for exons.

Source: wikipedia

     Alternative splicing is regulated by cis and trans-acting regulatory elements. Trans-acting regulators are proteins which affect the splicing of a given pre-mRNA molecule when binding to a specific position. Cis-acting regulatory elements are short sequences located in introns or exons and acting as enhancers or silencers of splicing. Depending on the cis-acting regulator present close to the splice site, the formation of the spliceosome will be activated or repressed. I am actually interested in studying these regulatory mechanisms during my PhD project. A detailed study about these regulators is also very interesting for medicine, we can improve the curation for different diseases related to a splicing mechanism.
     As you could see, alternative splicing is a very important mechanism for the cell. Studying the regulatory mechanisms will help us understanding how exactly the decision of the intron removal and exon inclusion is determined.
     For further reading, you can have a look at the following sites:

• EURASNET
• Alternative splicing in Wikipedia

Tags : Biology

Owncloud: your personal open-source cloud

23/03/2012 à 15:45 - No comments

     We are actually living in the cloud generation, and nobody can ignore it. You don't have to be a geek to understand what cloud computing means, because we are all directly or indirectly using cloud-computing services. Cloud-computing means the usage of a global machine (for storage or computation) rather than your local machine. We can cite iCloud, Dropbox or SkyDrive within many other cloud services for data sharing. With cloud computing you have access to everything (files, calendars, contacts, music, pictures...) in your cloud from everywhere with the only condition to have an internet connection. With the new generation of cellular data (3G), the rapidly developing 4G and many different free WiFi hot-spots, internet access is not a problem nowadays.
     In my case, I was using iCloud as a cloud-computing provider mainly because of my Apple-based environment (MacBook as laptop and iPhone as smartphone). I had all my calendars, contacts, reminders and iPhone backups data on iCloud and could access everything from my phone and my laptop. The only point I didn't like with iCloud and other cloud services is to be dependent from someone. If one day iCloud decide to close or change its privacy policy (see Google recently), I won't have my word to say. I prefer to use open-source and multi-platform tools when possible. I recently discovered Owncloud, which feets very well with my philosophy.
     Owncloud is an open-source alternative to all the cloud-computing or service providers. Once Owncloud is installed on a server, you can save all your data, calendars, contacts, music... and access everything from your computer or cell-phone using any web-browser. Owncloud is very easy to install and has a lot of very interesting features. The graphical user interface is beautiful. All the protocols used in Owncloud are very common and widely spreaded protocols such as webDav for file sharing, calDav for the calendars and cardDav for the address book. You can find a lot of different tools that support these protocols for all the existing computer or mobile platforms.
Owncloud integrates a PDF reader and a text editor function. The text editor can recognize many different programming languages and highlight the code you are writing. A music player is also available on Owncloud, after uploading your albums in Owncloud you can listen all your music within any web-browser without any additional tool

     Why I like Owncloud ?
     I am using a lot the calendars and contacts on my laptop and my phone, it is just a pleasure. It works very well on iPhone and Thunderbird. I am not limited on the disk space as I installed Owncloud on my own server. I am the only person with access to my data, but I can also give limited access to other people for some specific files for example. I can always modify or add a new function to Owncloud very easily with some basic programming knowledge.
     The actual version is number 3 and the version 4 is already on its way with some new features planned such as a Notes application and even an email provider. The community is growing every day and the forum is full of people willing to help for any question and open to remarks and suggestions. You can even propose your own application to the Owncloud community using their app database.

     Last but not least, you can try Owncloud without any installation here.

Tags : Software

How to get a standing ovation at your presentation

09/03/2012 à 19:00 - No comments

     During the SIB PhD Training Network retreat, I had the chance to participate to a talk from Dr. Philip Selby about “Training in Communication Skills”. Philip Selby is a doctor in Medecine (from Cambridge University) and is actually the head of PSA Consulting). Dr. Philip Selby is also a Distinguished ToastMaster (DTM). ToastMasters is a non-profit organization that teaches public speaking through a worldwide network of meeting locations. You can find the closest to your city on the website if you want to join. There are also some very interesting free resources available on their website.
     Here, I summarized the important points about preparing and giving a presentation in case it will be helpful for someone.
Please feel free to follow them

General tips

• The talk should be separated in three parts: the introduction, the body of the talk and the conclusion.
  
  • The introduction should be clear for the audience, they should know what you are going to talk about.
  • The body should contain a limited number of elements but not too much.
  • The conclusion should emphasis important aspects and remind people of the main points to remember. Be careful not to raise any new point in the conclusion.
• You can use a visual aid for your presentation. The most famous one is Powerpoint slides (I am using LibreOffice for mines). Be careful not to use too much slides because it will distract the attention of your audience, people should look at you and not your slides. Show slides only when it is really essential such as for diagrams or mathematical equations for example.
• Keep the time, don't finish after the limit time.
• Enthusiasm: show that you are very interested in what you are talking about.
• Know your audience: Take time before your presentation to meet your audience if it is possible or to know who they are. Chatting with people before the talk will give you the impression of doing the presentation for your “friends”.
• Manage your stress: You can be afraid of giving a talk, it is a very common reaction. The known “symptoms” are sweating (face, hands), palpitations, “butterflies” in stomach and empty brain... but preventive measures exist. To be less stressed 3 points are very important: practice, preparation and relaxation.
  
  • Practice: practice as much as you can your talk and presentation, always accept to give an in-promptu talk and consider it as an exercise.
  • Preparation: the only key-point is rehearsing.
  • Relaxation: do some abdominal breathing and small exercices.
  To be less nervous, it is good to know the place where you are gonna give the presentation. You can go to that place before the meeting starts to see where people will seat and where you are going to speak. Mental imaging can also help to manage your stress, you can imagine that you are giving a wonderful talk followed by a standing ovation. If you do so, there are more chances that it will happen.
  

The first impression

• The first impression you'll give to your audience is very important, because you have only one chance to give a good impression.
• Your appearance: the appearance depends on your dress. Don't dress worst than your audience.
• Your voice: try to know how your voice sounds before the presentation, you can ask for feedback from your friends. You can control the volume and the timing of your voice: don't speak at the same speed or same volume and don't be monotonous. Be careful of the articulation when speaking to a multicultural group, different nationalities or to people with different languages background. Make a pause after something important, let the audience digest what you said. With pauses, you will give to the audience the impression of anticipating what is next. Some people are saying "eee" or "mmm" a lot while speaking, you can try to say nothing (make a pause) instead.

The body language

• More than half of the communication is non-verbal. How you appeared to your audience will affect your presentation. Don't lean on a chair, seat on a table or keep your hands on your pockets. Take care of your posture. Do a little bit of movements and some gestures, it helps to reinforce what you are saying and emphasis the point that you are making.
• The facial impression is crucial: some people smile a lot when they are nervous (even when the topic is not hilarious).
• The eye-contact: Difficult when there is to much people. In that case do it with different people in different places. Don't look down or up to the audience. With eye-contact you can see what people are doing, you have indirect feedback. If they are smiling, they are enjoying and are with you. Be careful, eye-contact doesn't mean scanning.
• Mannerisms: repetitive movements the person is not aware of, for example swaying.

Responding to questions

• How you respond is very important: listen each question carefully and repeat the question to make sure you really understood. While answering, focus on the questioner.
• The reply should be as succinct and relevant as you can, don't give more information than the question.
• If a question is too long, choose a specific point of it.
• If you don't know the answer: don't invent something or don't make a guess. You can refer the question to the questioner like: "what do you think about it ?", "I don't thought about that, is there anyone in the audience who want to answer ?", or " I don't know I will look at it and send you an email".
• If someone wants to obsess you, this people is not interesting in getting an answer, he/she just wants to tackle you. Don't get to a fight, you will loose. Be very diplomatic and polite, try to answer as best as you can.
• If time is not enough: take one last question, don't prolong the situation. Use the last question to put on your last remark.

Tags : HowTo

The Raspberry Pi revolution

02/03/2012 à 19:53 - 5 comments

     After Apple, Blackberry, Pear ... comes the Raspberry revolution
     Wednesday February 29, 2012 was obviously a big day. The Raspberry Pi foundation just released the Raspberry Pi computer (RPi) that day at 6 AM (GMT), it was actually a first launch of 10,000 RPi.
     The Raspberry Pi is a credit card format computer at a very low price. Two models exist for the RPi: the model A for 25$ and the model B for 35 $. They both have a 700 Mhz ARM processor, 256 MB RAM, HDMI, USB, SD card, RCA video and Audio output connections. The model B has an ethernet port and one supplementary USB port. As operating system you will find an adapted version of Fedora (Unix-based operating system). You can see the differences between the two models on the following schema:



     The aim of the foundation was first of all to allow access to computer and internet for children and education mainly in poor countries. What is sure, is that they reached more than their initial goal.
A wide range of scenarios are possible for the RPi usage. First of all, the joy of discovering computers in poor countries. Second, it will be very interesting for a personal use. The RPi is really enough for a daily use, meaning word-processing, internet, mailing, pictures, movies (plays high definition video). Finally, it is a wonderful toy for all the geeks we are You probably all know about the Arduino which is a very small board that one can program and use in many different projects. Here, we have a complete computer between our hands for such a low price. One can use it as a media player, as a server, for robotics... It is easily possible to extend the RPi possibilities with WiFi USB sticks or a touchscreen for example. I am also convinced that we will be soon able to run Ubuntu or Android as operating system as well.
     I don't know what will be the response of all the other companies to these very low prices because the RPi will be far than enough for a lot of people as a personal computer. For sure the RPi misses a keyboard, a screen and a mouse but nowadays one can buy a complete set for less than 100 €.
     If you want to buy one now, I am sorry for you, it's too late. The first launch of 10,000 RPi was sold out right after few minutes its started. I am planning to buy one as soon as the first real tests are done. I will wait for feedback from early users. I registered at RS online and I will impatiently wait for a mail from them to got one...

     You can register here to try to get one.

Tags : Hardware

Sequence your own genome using a USB stick

22/02/2012 à 19:00 - No comments

     Sequencing became easier nowadays thanks to the high-throughput (or next-generation) sequencing. With these new sequencing methods, a single genome can be sequenced within few days or hours, depending on how big the genome is. This very powerful and high quality technology is based on the parallelization of the sequencing process generating millions of sequences at once. Thanks to the generalization of these methods, the prices were also pulled down but remains still expensive and not for individual use.
     Nanopore Technologies is a company based in Oxford and active on the sequencing area. Last week during the Advances in Genome Biology and Technology conference, Oxford Nanopore Technologies presented a new product to sequence any genome very rapidly and at a lower price. This module is named minION and presented as a simple USB stick. To sequence a genome, any sample such as blood or plasma should be enough. The sequencing will take place within the USB stick and the results available on your computer. A number of tools are provided to work on the newly sequenced genome.
     The sequencing protocol is based on a nanopore mechanism. A nanopore is a small hole (blue element on the picture) found in many cellular membranes. Depending on the pore, it allows some molecules to pass and blocks some others. Two methods are available for the nanopore based sequencing: the strand sequencing and the exonuclease sequencing.
     In strand sequencing, the nanopore will be coupled with an enzyme (green element on the picture) linked to the dna. The enzyme will open the double-stranded DNA and direct it through the nanopore. In exonuclease sequencing, the system is very similar. The DNA molecule is attached to the nanopore by the exonuclease which cleaves the DNA to single nucleotides passing through the nanopore. Each element passing the nanopore is analyzed, and a different signal specific to each nucleotides A, C, T or G is produced.
     At the end we obtain a whole sequence of signals translated to the corresponding DNA sequence. As an example, the researchers sequenced the genome of the PhiX virus composed by 5000 based pairs in few minutes. This technology can be used in medicine to quickly detect a genetic related disease for example or detection of viruses. The nanopore sensing works also with RNA, proteins and other small molecules. The product will be available soon for a price around 900 $.
     However, some points still need to be clarified. For example the minION should be for a unique run, which will results in higher price for multiple samples studies. Another point is about the quality. Actually the minION cannot sequence at a single-base sensitivity, the nanopore is reading three bases at a time and an algorithm is used to define the best matching sequence. The company announced that they are hardly working on trying to get a single-base sensitivity.
     As I mentioned, the minION still needs some improvements, but we can easily say that we are rapidly coming to a very-high-throughput-next-generation sequencing.

credits: piture from nanoporetech.com

Tags : Bioinfo

Integrating iCloud into Thunderbird

17/02/2012 à 19:22 - No comments

     Apple released a few months ago the latest version of the iDevices operating system iOS5. Among the different new features, iCloud was one of the most important. iCloud keeps all the iDevices and Mac computers synchronized for calendars, reminders, contacts, bookmarks... It also supports iDevices backup on the cloud.
     I am using iCloud since two months now, I like the idea of being synchronized everywhere, the calendars and reminders are very useful for me. I can find everything synchronized in my iPhone and my MacBook. You can access all your information at www.icloud.com and from your device using the existing applications such as iCal, Address Book or Mail for example. I don't like to use many different softwares when I can have everything at the same place from the same tool.
     I am using Thunderbird for a while now. Thunderbird is an open-source mailing application from the Mozilla group (the same as Firefox). Thanks to the incredible and always increasing number of add-ons, it is possible to easily extend the possibilities of Thunderbird. Here, I will explain how to use Thunderbird (I am actually using mac version 9.0.1) to access your iCloud mails, calendars, reminders and notes. The access will be read and write, so you can modify any element from Thunderbird or your iDevice and it will be synchronized in your iCloud account.
     To do so, you have to know the addresses of the iCloud servers you are using. For this step we will use an existing script from NiftySide. You can find this script here - please donate if you found the script helpful. By following the different steps, you will obtain the addresses for the servers you are using in iCloud. We will use these addresses into Thunderbird.

iCloud Mails and Notes
     I have a mail address using the @me.com domain. To add your iCloud mail account into Thunderbird create a new email account with the following information:
Imap server: p02-imap.mail.me.com
Username: Your name before @me.com
Smtp server: p02-smtp.mail.me.com
     You can then access all your iCloud mails and notes within Thunderbird.

iCloud calendars
Install the Lightning add-on in Thunderbird. You can download it here or directly from Thunderbird using the Tools/Add-ons menu.
     1 – Add a new Network calendar using the CalDav protocol
     2 – Use the address of your calendar you obtained from the previous script
     3 – Finish by choosing a color and a name for your calendar (you can use a different name than your phone)
     You can see your calendar on the list and you will probably access it only for a short moment To use the calendar correctly, you have to modify a configuration file. Don't worry it is not a big deal. You have to add some modifications on the following file:
/Users/[username]/Library/Thunderbird/Profiles/[$code]/extensions/[$code]/calendar-js/calDavRequestHandlers.js
for $code, you have to find which one correspond to your iCloud calendar if you have multiple calendars.

     4 – open the file with your preferred text editor (Aquamacs for me)
     5 – Add the following code at the exact line number 580 (respect the indentation)
    if (!r.getcontenttype &&
        r.href &&
        r.href.length >= 4 &&
        r.href.substr(r.href.length - 4,4) == ".ics") {
        // If there is no content-type for the resource but its name
        // ends with ".ics" assume the content type to be
        // text/calendar. Apple iCloud interoperability fix.
        r.getcontenttype = "text/calendar";
    }

     6 – Add the following code to the line 609
    r.status.indexOf(" 200") || // Apple iCloud returns 200 status for each item
     7 – Save and close the file
     8 – Restart Thunderbird and enjoy
     We need this workaround because of the specific extension of iCal calendars. Now, Thunderbird recognizes the extension .ics as a calendar. You can also add your reminders by following the first 3 steps and using the corresponding iCloud server address. If you have any question or remark don't hesitate to contact me.
     Unfortunately, I didn't find any add-ons for the CardDav protocol to synchronize my contacts. I can access my Mac address book within Thunderbird but cannot modify it, the access is read-only.
     I really like iCloud and the cloud in general but of course I would prefer something more open. I recently discovered OwnCloud and I am actually trying it. I am planning to discuss about OwnCloud in another post.

Tags : HowTo

Siri Fail

09/02/2012 à 18:21 - 3 comments

Voici une affiche électorale que j'ai eu l'occasion de voir près de la gare de Lausanne. Je dois avouer que j'apprécie ce genre de détournement.

Tags : Fun