BioGeek

DeepPCB has an AI autorouter [1] that uses reinforcment learning and works really well. Recently they also released an AI agent that analyzes your board, proposes plans and can route your board for you [2]. They have a KiCad plugin [3] and you can try it for free.

[1] https://deeppcb.ai/reinforcement-learning-pcb-routing-explai... [2] https://deeppcb.ai/cooper/ [3] https://deeppcb.ai/deeppcb-kicad-plugin-ai-pcb-routing/

Disclaimer: I work at InstaDeep, the company behind DeepPCB, but I don't work on this product.

Here it is:

https://chemrxiv.org/engage/chemrxiv/public-api/documentatio...

> Also can we train this same model on regular language data so we can converse about the genomes?

Yes! That is what has been done in ChatNT [1] where you can ask natural language questions like "Determine the degradation rate of the human RNA sequence @myseq.fna on a scale from -5 to 5." and the ChatNT will answer with "The degradation rate for this sequence is 1.83."

> My biggest point of confusion is what type of practical things these models can do.

See for example this notebook [2] where the Nucleotide Transformer is finetuned to classify genomic sequences as two of the most basic genomic motifs: promoters and enhancers types.

Disclaimer: I work at InstaDeep but was not involved in either of the above projects.

[1] https://www.biorxiv.org/content/10.1101/2024.04.30.591835v2 [2] https://github.com/huggingface/notebooks/blob/main/examples/...

For a recently published example of this see [1]: an automated platform, called Self-driving Autonomous Machines for Protein Landscape Exploration (SAMPLE), can design and build proteins using AI agents and robotics. In an initial proof-of-concept, it was used to make glycoside hydrolase (sugar-cutting) enzymes that can withstand higher-than-normal temperatures.

The SAMPLE system used four different autonomous agents, each of which designed slightly different proteins. These agents search the fitness landscape for a protein and then proceed to test and refine it over 20 cycles. The entire process took just under six months. It took one hour to assemble genes for each protein, one hour to run PCR, three hours to express the proteins in a cell-free system, and three hours to measure each protein’s heat tolerance. That’s nine hours per data point! The agents had access to a microplate reader and Tecan automation system, and some work was also done at the Strateos Cloud Lab.

SAMPLE made sugar-cutting enzymes that could tolerate temperatures 10°C higher than even the best natural sequence, called Bgl3. The AI agents weren’t “told” to enhance catalytic efficiency, but their designs also had catalytic efficiencies that matched or exceeded Bgl3.

[1] https://www.biorxiv.org/content/10.1101/2023.05.20.541582v1 [2] https://www.readcodon.com/i/122504181/ai-agents-design-prote...

I have a DonkeyCar [1] with a Jetson Nano 4GB. Is it possible to follow the course with that hardware platform?

[1] https://www.donkeycar.com/

There is a small error in the code. The variable `count` should be defined on line 11 like:

    count = int(record["Count"])

en the appearance on line 15 should be removed.

All those pages that you found of people having exactly that same combination of educational background can be simply explained. They are the default sample content of the Team page on certain Wordpress themes (Therefore also the WP in ‘Blockchain WP’). A quick Google search shows that for example the FinanceCo theme from Radius has the same exact Education listing.[0]

So the other profiles you found could just be sloppy webmasters who didn't remove the default Team pages of their Wordpress theme.

[0] https://www.radiustheme.com/demo/wordpress/themes/financeco/...

Using Biopython. Note that the search query that I am using currently returns 70605 results, so you might want to tweak it fit your needs.

    from Bio import Entrez
    import time
    from urllib.error import HTTPError
    
    DB = 'nucleotide'
    QUERY = '("pneumoviridae"[Organism] OR "Coronaviridae"[Organism])'
    
    Entrez.email = 'your.email@provider.com'
    handle = Entrez.esearch(db=DB, term=QUERY, rettype='fasta')
    record = Entrez.read(handle)
    
    handle = Entrez.esearch(db=DB, term=QUERY, retmax=count, rettype='fasta')
    record = Entrez.read(handle)

    id_list = record['IdList']
    count = len(id_list)
    post_xml = Entrez.epost(DB, id=",".join(id_list))
    search_results = Entrez.read(post_xml)
    
    webenv = search_results['WebEnv']
    query_key = search_results['QueryKey']

    batch_size = 200
    with open('viruses.fasta', 'w') as out_handle:
        for start in range(0, count, batch_size):
            end = min(count, start+batch_size)
            print(f"Going to download record {start+1} to {end}")
            attempt = 0
            success = False
            while attempt < 3 and not success:
                attempt += 1
                try:
                    fetch_handle = Entrez.efetch(db=DB, rettype='fasta',
                                                 retstart=start, retmax=batch_size,
                                                 webenv=webenv, query_key=query_key)
                    success = True
                except HTTPError as err:
                    if 500 <= err.code <= 599:
                        print(f"Received error from server {err}")
                        print("Attempt {attempt} of 3")
                        time.sleep(15)
                    else:
                        raise
            data = fetch_handle.read()
            fetch_handle.close()
            out_handle.write(data)

Trammell Hudson in 2009 reverse engineered the firmware of the Canon EOS 5D Mark II because he was frustrated with some of the limitations in the camera's firmware when making short films. That little hack turned into Magic Lantern. On his website [1] you'll find a screenshot [2] of his first success: adding three extra vanity letters to the firmware version number. He states: "Re-writing strings is a good easy technique for figuring out if you have 'won' and your code is running on the system."

[1] https://trmm.net/Taking_things_apart#Extending [2] https://www.flickr.com/photos/osr/16412008471/lightbox/

This list highlights the most import organisms that have their genome sequenced, but look at [1] to see the full list of 22244 organisms that are currently sequenced.

Most human pathogens, like Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Salmonella enterica, Mycobacterium tuberculosis, ... have several thousand assemblies each.

[1] https://www.ncbi.nlm.nih.gov/genome/browse/

Several good answers can be found on http://mathoverflow.net/q/95865 and http://math.stackexchange.com/q/45594/14018

> The game would be probably to provide some kind of standard or API that would make all those independant providers rally accross a common model.

This common specification already exists. It is called GTFS [1] (General Transit Feed Specification) and can be used to exchange static transit data. There is also GTFS-realtime [2], an extension to GTFS, to be used to exchange realtime transit data.

The specification was designed through a partnership of the initial Live Transit Updates partner agencies, a number of transit developers and Google. The specification was introduced and released under the Creative Commons Attribution 3.0 license in August 2011.

[1] https://developers.google.com/transit/gtfs/ [2] https://developers.google.com/transit/gtfs-realtime/

The latest sport where Sportvision used this technology is sailing, called LiveLine there. During the last America's Cup [1] they used it to show the starting, finish and boundary lines, distance between the boats,...

[1] http://youtu.be/r0LH5cCuc_4

Some more things you could ask in this article by Hacker School alumna Julia Evans [1] and this article on Runtime Era [2].

[1] http://jvns.ca/blog/2013/12/30/questions-im-asking-in-interv... [2] http://www.runtime-era.com/2013/03/my-interview-questions-fo...

> If he could write it up in a blog, OkTrends-style, I feel like it could get a huge number of hits

He released a 37 page eBook with an easy-to-implement blueprint: http://www.amazon.com/dp/B00HY351S2

> I would imagine that there's hardly a comprehensive database of a DNA of all existing life forms on Earth.

An annotated collection of all publicly available DNA sequences is available from the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. They are basically all three the same database and they exchange updates on a daily basis. However, small timelags in propagating data between the database centers causes minor differences.

Also see the discussion at the bioinformatics subreddit: http://www.reddit.com/r/bioinformatics/comments/179e9k/a_far...

Biostars.org is a stackexchange-like site for bioinformaticians.

See there for answers to your question, eg:

* Best resources to learn molecular biology for a computer scientist. [1]

* What are the best bioinformatics course materials and videos (available online)? [2]

[1] http://www.biostars.org/p/3066/

[2] http://www.biostars.org/p/10766/

Some guys in Russia have done something similar. They have released a 360° aerial panorama [1] from the stratosphere. They have also been experimenting with 360° video [2] and provide detailed instructions on how they achieved their results.

[1] http://www.airpano.com/360Degree-VirtualTour.php?3D=Stratosp... [2] http://www.airpano.com/Articles-AirPano.php?article=101606

You can use TunesViewer [1] to view iTunesU media and podcasts in Linux.

[1] http://tunesviewer.sourceforge.net/

Kevin Kelly has an extensive collection of what he calls True Films [1]: "I define true films as documentaries, educational films, instructional how-to's, and what the British call factuals - a non-fiction visual account."

He has also released an ebook where he offers rave reviews of 150 great true films. Each film gets a short review of why it is worth your time, and then features 4 or 5 screen grabs from the film to show you what the texture and style of the film is. It also includes a picture of the cover and indicate where you can rent it (say on Netflix) or purchase it (from Amazon).

What is he looking for in a great true film? "It must be factual. It must surprise me, but not preach to me. If it introduces me to a world or subculture that I never thought about before, even better. There's a plot - a transformation from beginning to the end."

[1] http://truefilms.com/ [2] http://www.kk.org/books/true-films.php

My Python answer for the second question, where `post` is patrio11's post as input:

    from  collections import defaultdict
    from string import ascii_letters

    d= collections.defaultdict(int)

    for letter in post:
        d[letter] += 1

    print [letter for letter in sorted(d, key=d.get, reverse=True) if letter in ascii_letters][2]

Any comments on improvement for readability or conciseness?

jeroen.vangoey@gmail.com (I have also updated my profile page, sorry about that).

I'm looking forward to any questions you might have.

Work as a deckhand on a superyacht. The responsibilities of a deckhand include cleaning, varnishing and painting, polishing, tender operations (small-boat handling skills required) and working the lines/ropes. This is a hard work position with long hours, but can have the added benefit of substantial tips on the larger and busier charter vessels.

Typical salary can be found here: http://www.superyacht-crew-academy.com/salaries_superyacht_c...

I work on a 78ft yacht in the Med, (http://www.camperandnicholsons.com/sales/search/-/page/sales...), PM me if you want more details about this kind of work.

The health department of the stae of New York considers 23andMe’s genome scan to be a medical test that must be approved by regulators and ordered by a doctor.

A competing company, Navigenics, successfully applied to have its test licensed in New York. It has essentially put aside marketing to consumers, aiming instead at doctors. It is also courting corporations that might use the test as part of their employee wellness programs.

http://www.nytimes.com/2010/03/20/business/20consumergenebar...

Here is a slideshow of some panoramas I made with Hugin: http://www.flickr.com/search/show/?q=panorama&w=27429469...

Side-by-side view of the 2 psalms in a diff viewer: http://i.imgur.com/ipaPW.png

That's the one I was looking for. Thanks!

Ben Fry (of Processing fame)'s PhD thesis: "Computational Information Design".

Abstract:

The ability to collect, store, and manage data is increasing quickly, but our ability to understand it remains constant. In an attempt to gain better understanding of data, fields such as information visualization, data mining and graphic design are employed, each solving an isolated part of the specifi c problem, but failing in a broader sense: there are too many unsolved problems in the visualization of complex data. As a solution, this dissertation proposes that the individual fi elds be brought together as part of a singular process titled Computational Information Design.

This dissertation first examines the individual pedagogies of design, information, and computation with a focus on how they support one another as parts of a combined methodology for the exploration, analysis, and representation of complex data. Next, in order to make the process accessible to a wider audience, a tool is introduced to simplify the computational process for beginners, and can be used as a sketching platform by more advanced users. Finally, a series of examples show how the methodology and tool can be used to address a range of data problems, in particular, the human genome.

http://benfry.com/phd/

This is good advice, but in practice I find it very difficult to translate these tips if you don't have to sell a product/service.

Case in point, recently I was asked for a job interview to "prepare about 10 slides as a short training session on the use of the Ensembl Genome browser by wet bench lab scientists".

I tried to use the techniques described in this presentation and at presentationzen (http://www.garrreynolds.com/Presentation/slides.html) (use high quality graphics, limit bullet points, choose your fonts with care,...). My result is here: http://dl.dropbox.com/u/138632/EnsembleGenomeBrowser.odp (OpenOffice Presentation file, since it is a very visual presentation see the notes for the accompanied text).

The problem I ran into is that I had to use lots of screenshots of the Ensembl Genome browser to tell how it worked. I tried to make those screenshots as pretty as possible (maybe even too cliché with the fading mirror effect) but I din't find much room to show my passion for bioinformatics. Any advice on what I could have changed?