Online Lab Notebook?

For people like me who have always used a paper-based laboratory notebook to keep track of my experiments and notes, the idea of using an Electronic Lab Notebook online seems a bit odd at first. But, it also has that slightly neat feel to it too.

Purple Corn Husks and And Anthocyanin Water

I guess i can now be considered a DIY scientist or maybe a Citizen Scientist now, considering how many crazy things i seem to be pursuing these days. I’m already subscribed to the DIYbio mailing list, which often has very interesting discussions, and many of those are way over my head in terms of technical knowledge.

Still, in this age of Interconnectivity and social blogs, people wan’t to know what kinds of cool things your experimenting with. Cool is a relative term i suppose though, and interests vary. For a few days i’ve been trying to use the powers of Google to help me find a really good (and free) online lab notebook. Ideally one with the ability to use OCR software to recognize text in any photos i upload. I only really found two free ones that i was willing to consider. The rest seemed designed for a whole group of people in a lab, and cost lots of money.

1. The first option is hosted on OpenWetWare, and is a simple wiki. For most people this is the best option, and apparently is what the IGEM teams now use for their lab journals. It’s actually really good, but doesn’t have any OCR indexing software. This is the one i am now using. The only “downside” is that it has a small learning curve to figure out how formatting works on a wiki. If you’ve ever edited wikipedia before, you might already know how.

2. The second option is called Evernote. It’s a note taking platform with sharing options available. It has a free version, but it kindof sucks, and wants you to pay for a pro version. I have my doubts the pro version would be worth it. I must admit that while testing it out, i almost ran out my allowed uploads for the month. Thats the part that really soured it for me, especially when combined with odd designed interface. It’s actually not that bad, but not what i was looking for. I was interested in Evernote because it looked like it might have a good interface, and boasted about an image indexing feature that essentially uses some sort of OCR tool. The OCR feature does work… but the whole interface is slow and clunky. It also didn’t display the search results in a friendly way.

Here is the test notebook i was testing with my evernote account if you want to see what it looked like. Just be sure to know that i have now migrated to using OpenWetWare’s wiki, and will be using that from now on. Here is my online notebook: http://openwetware.org/wiki/User:Andrew_Barney/Notebook

 

But in truth i think i prefer paper notebooks to any offering online. This is a nice printable one: here.

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Do plants really need sunlight?

Electricity plays a vital role in plants. Usually in the form of Sunlight or Electromagnetic Radiation. Research workers are finding evidence that plant cells’ sensitivity to electric current can be exploited to enhance their growth.

Plants use Chlorophyll to produce their own energy for growth. But, what if we could grow plants faster by giving them a second source of energy (electricity)? Or what if we could grow plants completely in the dark by supplementing them with DC or AC current without giving them any sunlight at all?

 

A conductive helical coil is spaced around the stem of a plant

 

…It turns out, that we might be able to.

A while back i got the idea out of nowhere that we might be able to grow plants in the dark by giving them electricity instead. This led me on a deep quest to find out if anyone else had asked this question before. Long hours spent on Google produced some interesting results, which i forgot about until recently. It’s always been in the back of my mind.

I found several interesting results. One article i read, stated that a researcher had done experiments on trees in California, and discovered that they produce small amounts of electricity. At least i think it was California. A quick google search now, produces mixed information. Apparently researchers from Washington, Boston, Massachusetts all claim to have discovered that trees can produce electricity. So, who knows who discovered it first.

The next interesting idea is that by creating an alternating current through a coil around the stem of a living plant, results with the plant growing taller and larger, with more numerous and larger leaves, under otherwise normal growing conditions . That by itself is incredibly fascinating. It’s even got a patent!

“It is generally known that many types of life forces are affected by electrical phenomena. For example, proposals have been made to pass electrical current through the soil to regulate the growth of plants.

It has been found that passage of alternating current through a coil disposed closely around the stem of a living plant, and thereby subjecting the plant stem of induced EMF, results in significant modification of growing characteristics, with the plant growing taller and larger, with more numerous and larger leaves, under otherwise normal growing conditions .”

The third interesting experiment i uncovered was very close to the previous one. But instead used DC current applied to the plants root system. It not only goes on to state that the DC current increases growth like the precious one, but also states that plants were able to survive in the dark by feeding on the electricity instead of the sunlight. If true, this opens up whole new possibilities of growing food indoors or underground, without the need for expensive lighting. It might also help so our houseplants don’t die from lack of sunlight, like they normally do. (i couldn’t find the original research paper, but this seems to be the exact same info, and includes the idea of using a solar cell)

The last idea is about using ultrasonic sound waves to promote better plant growth. Apparently it seems it’s also well documented that plants can be affected both positively and negatively by certain frequencies. Even to the point of death in some cases. I honestly didn’t read much about the ultrasonic, because i was more interested in the other attempts. But, here is the info anyway.

I think i might attempt to build a helical coil, and attempt if i can successfully grow a plant inside during the winter. I’ve tried planting some plants indoors before, but because of the low amount of light they seem to die rather quickly. I may also try placing one of these around a corn plant in the spring, and seeing if it grows larger and taller than the rest.

FIRST Robotics Open Source Electronics

After spotting an article on MAKE about NASA providing a huge $20 Million grant, i realized that many people might not know that FIRST Robotics now releases their electronic designs in true Open Souce spirit.

I’m no longer involved in FIRST, but during my last year i wrote FIRST a letter explaining how i thought they needed to adopt an open source credo. My letter didn’t cause a revolutionary change, but i did receive a response that was a bit unexpected. It turns out that more than a few were impressed with my letter, and decided to release all their electronics designs in the public domain. Including CAD files, PCB designs, and Schematic diagrams. Like i said, not a huge change, but a step in the right direction.

http://www.usfirst.org/roboticsprograms/frc/control-system-resources

I’m not sure if their software is still mostly proprietary or not. But, i do think there are multiple programming languages available, and perhaps they are cross-platform. That seems like a step in the right direction too. 🙂

Kio estas IGEM?

IGEM logotipo

[eo]

La Internacia Genetike Inĝenierita Maŝino (iGEM) konkurso estas tutmonda Sinteza Biologio konkurso celanta de la bakalaŭra nivelo studentoj.

Unu celo de la konkurso estos provo konstrui simplaj biologiaj sistemoj de normo, interŝanĝeblaj partoj kaj uzi ilin en vivanta ĉeloj. La iGEM konkurso facilig ĉi tiu de provizanta biblioteko de normaj partoj (nomita BioBriko normo biologiaj partoj) al studentoj, kaj peti ili al dizajno kaj kontrui genetikajn maŝinojn kun ili. Studento teamoj ankaŭ povas submetiĝi sian propran BioBrikoj. Sukcesaj projektoj produktas ĉelojn ke elmontr nova kaj nekutimaj nemoveblaĵoj de inĝenierado aroj da multoblaj genoj kune kun mekanismoj reguligi ilian esprimon. Informoj pri BioBrick normo biologiaj partoj, kaj ilaro al far kaj manipul ili, estas proviz de la Registrejo de Normo Biologiaj Partoj, aŭ simple, la Registrejo. Ĉi tiu estas kerno rimedo por la iGEM programo, kaj tiu, kiu estas evolu rapide al plenum la bezonojn de la programo.

[en]

The International Genetically Engineered Machine (iGEM) competition is a worldwide Synthetic Biology competition aimed at undergraduate university students.

One of the aims of the competition is to attempt to build simple biological systems from standard, interchangeable parts and operate them in living cells. The iGEM competition facilitates this by providing a library of standardized parts (called BioBrick standard biological parts) to students, and asking them to design and build genetic machines with them. Student teams can also submit their own BioBricks. Successful projects produce cells that exhibit new and unusual properties by engineering sets of multiple genes together with mechanisms to regulate their expression. Information about BioBrick standard biological parts, and a toolkit to make and manipulate them, is provided by the Registry of Standard Biological Parts, or simply, the Registry. This is a core resource for the iGEM program, and one that has been evolving rapidly to meet the needs of the program.

Source / Fonto:

http://eo.wikipedia.org/wiki/IGEM

http://en.wikipedia.org/wiki/IGEM

Chemistry in Esperanto

 Kemio en Esperanto

Gxenerala, Organika kaj Biologia Kemio
Gxenerala, Organika kaj Biologia Kemio

Success! Well, okay… only a minor success, but still. I finally managed to track down a PDF copy of “General, Organic, and Biological Chemistry” in Esperanto (Gxenerala, Organika, kaj Biologia Kemio). Yes Finally! After months of trying to track it down on the internet. I finally contacted an Esperanto speaker in Columbia, who gave me a link to the only working torrent.

http://isohunt.com/download/70393117/2afe090c0ce000911d7c89f499858d01ef8033a1.torrent

Sukceso! Bone, okaj… nur malgranda sukceso, sed ankoraŭ. Mi fine sukces ..mi trovis .PDF kopio de “Ĝenerala, Organika, kaj Biologia Kemio” en Esperanto (Gxenerala, Organika, kaj Biologia Kemio). Jes Fine! Post monatoj de provanta spuri ĝi en Interreto. Mi fine kontaktita Esperantoparolanton en Kolumbio, kiu donis min la korekto ligon por torento.

I originally found out about that book (Gxenerala, Organika, kaj Biologia Kemio) after doing a random search about the -ENZO suffix, and how it originated. That search led me to the reference to the translation of the book by the Chicago Esperanto Society. So, logically you would think that by contacting the Chicago Esperanto Society, would pave way to obtaining a copy…

sakarozo, glukozo kaj fruktozo
sakarozo (sukero - sukrozo), glukozo kaj fruktozo

…NOPE. They had never heard of it, nor had any copies. I’m not sure why it was so hard to track down, but alas i’m happy i found it. Now the work can continue on being able to translate Penumbra Overture into Esperanto. And eventually my original goal of translating the Golden Book of Chemistry Experiments into Esperanto as well. I’ve already translated the cover. It reads “La Valora Libro da Kemiaj Eksperimentoj”.

Valora Libro Da Kemiaj Eksperimentoj
La Valora Libro Da Kemiaj Eksperimentoj

I’m still not that great at Esperanto, and still haven’t learned enough about the grammar, but I’m getting better at as time goes on.

and here is an interesting demonstration about combustion in chemistry by Daniel Solomon.

Kaj tio estas interesa klarigo de bruligxo esperante en kemia fakultato de Varsovia Politekniko je 14/12/07 de Daniel Salomon.

Alan Kapuler Lecture

An awesome lecture from Alan Kapuler. If you have any interest in sustainable agriculture, plant genetics, heirloom plants, Ecology, etc… I suggest you watch this lecture. You may also want to take a visit to the Homegrown Goodness plant forum. You might have to search through everyone’s blogs to get to some of the really good information, but it’s totally worth it. Everybody share’s seeds, and is committed to providing the best information available about practically any topic your interested in.

Edit:

http://untitled.pnca.edu/multimedia/show/854/

At the bottom is a tiny bar with the full audio.

The full audio is about 2 hours long. It’s fantastic. I highly suggest you take the time to listen to it all. 🙂

wordpress themes?

So, i’m experimenting with wordpress themes now. I never really cared what my blog looked like. But, hey i figured it probably would be easier to read/find stuff with a theme. If you have any suggestions, let me know. Otherwise, i’m going to try this one for awhile. It’s called “motion”.