Bioinformatica e Web 2.0

Inside Bioinfo

25 marzo 2009 - 10:57

Database Vettori

Dove cercate le mappe dei vostri vettori? Su Google? Su Pubmed?

Io mi sono trovato molto bene con questo Database di Vettori gestito da AddGene.

Fornisce molte informazioni sui plasmidi: sequenza, mappa, enzimi di restizione, proteine trascritte e tradotte, Il Bitcoin si divide a metà e nasce il Bitcoin Cash. Si possono depositare (gratuitamente) i plasmidi che sono stati utilizzati (ad esempio) in un lavoro, e questi possono essere acquistati da altri ricercatori.

Addgene è un organizzazione no profit, ovviamente i guadagni vengono usati per mantenere il servizio. Insomma…è una sorta di banca/database di vettori per aiutare i Ricercatori….

For other related information, if you need plastic surgeon, checkout Dr. Matthew Galumbeck.
Link: MyBioinformatica

Tags: bioinformatica, Database
24 marzo 2009 - 19:59

Disegnare velocemente Primer con CLC…

A seconda del tipo di PCR che si deve fare (Real Time Pcr o no, da genomico o da plasmide) si devono costruire primer più o meno “accurati”. Se si deve fare una Pcr da genomico ad esempio bisogna stare attenti che i primer non vadano anche ad annilare in altri punti del genoma, oltre a quello di interesse…

Nel mio caso faccio molte PCR da plasmidi. In questo caso le coppie di basi non sono molte, quindi è altamente improbabile che primer lunghi 15-20 nucleotidi vadano ad annilare in più punti.

In questo caso disegnare dei primer è molto semplice…Ma troppe volte vedo persone che disegnano su carta i primer, sia forward che reverse (perdendo tempo e rischiando di fare errori).

La cosa è molto più semplice con CLC Sequence Viewer:

  • (Ovviamente) Importare la sequenza del gene su cui fare la PCR in CLC Sequence Viewer
  • Selezionare lo spaziamento ogni 3 nucleotidi scegliendo il frame appropiato (Potete anche salvare questa opzione in modo da non selezionarla ogni volta).

schermata-clc-sequence-viewer-save-setting1

  • Selezionare i 15-20 nucleotidi che formeranno il primer FW (tenendo conto del frame e che devono terminare con una C o G), poi tasto dx -> Open Selection in new view
  • Tasto dx sul primer appena creato -> Select Sequence, di nuovo tasto dx -> Edit. In questo modo potete modificare la sequenza, aggiungere codoni di start, enzimi di restrizione.
  • Tornando sulla sequenza del gene selezionate il segmento che andrà a formare il primer Reverse. In questo caso non c’è bisogno di tenere conto del frame. Fate in modo che cominci con una G o una C (l’inizio che selezionate diventerà il 3?, quindi rappresenta la fine del primer). Al solito, fate tasto dx -> Open Selection in new view. Poi modificate il primer a vostro piacere aggiungendo codone di STOP o siti di restrizione.
  • A questo punto nella toolbox “Reverse Complemente Sequence” e avrete il vostro primer Reverse pronto.

schermata-clc-sequence-viewer-toolbox

I primer possono essere copiati-incollati sul sito dove ordinate i primer (evitate errori di battitura), possono essere stampati o salvati in una cartella. Vi ricordo che se si deve fare una Pcr da genomico bisogna stare attenti che i primer non vadano anche ad annilare in altri punti del genoma, quindi questo metodo non va bene (in questo caso c’è il sistema descritto da Nico).

Spero però sia utile a qualcuno!!

Alla prossima…

Link: MyBioinformatica

Tags: bioinformatica, how-to
16 dicembre 2008 - 20:04

Editor di sequenze: CLC Sequence Viewer

Un editor di sequenze è un programma in grado di manipolare con facilità sequenze nucleotidiche e proteiche. Il primo dei programmi che ho intenzione di presentarvi è CLC Sequence Viewer che è arrivato alla versione 5.1.1

Il programma è creato dalla CLC bio, che permette il download e l’utilizzo gratis, indubbiamente presenta una grafica molto curata, ed una facilità d’uso impressionante, adatto anche a chi non sa bene usare il computer.
Questo programma presenta tante limitazioni rispetto agli altri programmi (a pagamento) della CLC bio.
Le operazioni possibili sono (e le limitazioni relative sono):

  • effettuare ricerche direttamente su NCBI, anche se a causa delle limitazioni non è possibile effettuare ricerche su altri database, bisogna comprare le altre versioni.
  • creare allineamenti multipli e relativi alberi, con vari algoritmi: Clustal, T-coffe, ecc…
  • varie operazioni con i nucleotidi: convertire Dna <-> Rna, vedere filamento complementare di una sequenza, tradurla in proteina, Cercare ORF, ecc…
  • Cercare enzimi di restrizione presenti in una sequenza ed elencarli in una lista.

Quando si effettua una ricerca su NCBI, o si importa una sequenza, CLC Sequence Viewer è in grado di leggere le annotazioni e visualizzarle graficamente, indicando ad esempio promotori, la sequenza codificante in un cDna, domini e così via…Una grossa limitazione che ho trovato è non poter modificare le annotazioni riguardanti le sequenze. Quindi non è possibile selezionare una serie di nucleotidi/amminoacidi e aggiungere un’annotazione ad esse (ad es. questo è un promotore, qui c’è un sito di fosforilazione, ecc). Questa forte limitazione (e il fatto che secondo me i programmi dovrebbero essere liberi) mi ha spinto a cercare un altro editor di testo.

Qui è presente l’elenco completo delle limitazioni, paragonate ai relativi software a pagamento.

Il programma è disponibile per Windows, Mac, Linux (sia file .rpm che .sh), ed è molto semplice da installare.

9 dicembre 2008 - 09:00

How to Get Rid of Fleas in Your House, in Your Yard, and More

Fleas are some of the most annoying pests to deal with. They’re small, jumpy, and multiply quickly. Pets can pick up fleas from being outside in nature, around other animals, or when humans track in the insects on our shoes or clothes.

Excessive itching and scratching is a telltale sign your pet may have fleas. You may even spot the little acrobats. On average, fleas are 2-4 millimeters long, making them visible to the naked eye.

If your family pet has fleas, it’s likely that your yard and house will become a breeding ground. Acting quickly is key to preventing spread.

A flea infestation can test your patience and require persistence. But you can eradicate the problem with a combination of cleaning methods, sprays, and pet-friendly topical medications among other options.

Do fleas bite people, too?

Yes! Fleas are after blood and can bite people or latch onto our clothes or shoes. However, they really do prefer animals. Pets are ideal hosts because thick fur provides plenty of shelter for fleas to latch onto skin and feed, or lay eggs.

If fleas do bite you during an infestation, it will likely be around your ankles, or in folds of skin. Flea bites can cause an allergic reaction in the form of hives.

 

According to the Centers for Disease Control, the life cycle of the fleaTrusted Source depends on a lot on environmental conditions. Fleas flourish in warm climates and usually (but not always) die in the winter season.

Flea eggs are small but can be seen if you’re looking closely. They are smooth and white or light in color. A single adult female flea can produce up to 2,000 eggs in her lifetime. These eggs may be laid in your pet’s fur, deep in the carpet, or in tall grass.

In ideal conditions, fleas will evolve from egg to adult within 2 to 3 weeks. Adult fleas can live up to 100 days.

Fleas are ready to feed within a day of hatching, and begin to suck blood within 10 seconds of landing on a host.

If the weather isn’t ideal and there isn’t a host to feed on, flea larvae may remain dormant for months while waiting for better conditions to develop. This is a key reason dealing with infestations can be so difficult.

How long does it take to get rid of fleas?

The length of time required to get rid of a flea infestation depends on your environment, and how long the fleas have been there.

Prompt cleaning and using topical flea medications for your pet may get rid of the majority of fleas within a day or two. However, it can take days to weeks for all the fleas present in an environment to die, even with the most conscientious approach.

Fleas lay a lot of eggs very quickly, and some fleas have developed resistance to medications and insecticides. If you have a large property or multiple pets with fleas, it may take longer to get rid of the problem. The key to handling fleas is persistence.

How to get rid of fleas in your home

If your pet is a walking carrier of mature fleas, your home can become the nursery.

Since the flea has multiple life stages (egg, larvae, cocoon, adult), when adult fleas are present, it is assumed all of these stages are also present throughout your house. This means that you have to tackle the problem from all angles in order to truly eradicate the infestation. Learn more detailed information from this flea and tick prevention for dogs article.

To do this, you must treat your pet and its living environment at the same time. Depending on your pet’s boundaries, this may include your whole house or yard.

The Environmental Protection Agency (EPA) recommends the following cleaning approaches:

  1. Use a powerful vacuum on any floors, upholstery, and mattresses. Cracks and other tight spaces are usually good hiding places for fleas and their cohort of eggs, larvae, and cocoons. If you can, use a vacuum with a bag you can dispose of without coming into contact with its contents.
  2. Employ a steam cleaner for carpets and upholstery, including pet beds. The combination of high heat and soap is the enemy of fleas in all stages of life. Pay special attention to any spots where your pet usually lies down or spends a lot of time.
  3. Wash all bedding, including your pet’s, in hot water and detergent. Dry it at the highest heat setting. If the infestation is severe, consider getting rid of old bedding and starting anew.

The advent of topical flea treatmentsTrusted Source for pets have made insecticides pretty outdated. Topical prescriptions stop or augment the flea’s reproductive cycle and rapidly kill an infestation.

If you do aim to use an insecticide or other chemical cleaning treatment, please proceed with caution. Many are toxic to humans, pets, and the environment.

Here are some tips:

  • Aerosol sprays are recommended over foggers, as you can direct the spray under beds or other places that the foggers may be unable to reach.
  • Choose an insecticide that contains both an adulticide (kills adult fleas), such as permethrin, and an insect growth regulator (kills the eggs, larvae, and pupae), such as methoprene or pyriproxyfen.
  • People and pets shouldn’t come into contact with an insecticide or chemical treatment until it has dried. Be sure to wear gloves when you apply the spray, and only do it when everyone is out of the room or house.
How to get rid of fleas in your yard

The best way to eliminate fleas from your yard is to think about where they’re most like to hide.

Fleas love places that are:

  • shaded
  • humid
  • warm

Direct sun-exposed areas can get too hot, so you probably won’t find many fleas there. Problem areas will likely be found by observing where your pet likes to lie down.

Once you have your target zones, here’s what you can do to eliminate the fleas:

  1. Mow your lawn regularly and rake the exposed surfaces thoroughly. Fleas like to hide in tall grass. Make sure to bag the contents rather than add them to your compost pile.
  2. Remove debris, such as dead leaves and twigs, from flower beds and from under any bushes. Expose as much of the shady areas to sunlight as you can.
  3. Spread cedar chips on the areas where your pet likes to lie down, under the bushes, and on flower beds. Fleas hate the smell! Sulphur (powder or liquid) is also known to repel fleas and prevent hatching.
  4. Ask your local gardening center about nematodes, small worms that can eat insect larvae.
  5. Avoid overwatering. This can create the exact humid conditions for fleas to thrive in.
  6. Evict wildlife. Animals like opossum, mice, and squirrels can all carry fleas. It’s possible to repel these animals from your yard without trapping or killing them. The Humane Society recommends “gently harassing” animals to get them to move. This can include setting up barriers in the yard, putting up bright lights, playing loud music, and leaving rags soaked in cider vinegar.
Tags: bioinformatica, how-to
18 settembre 2008 - 09:00

Proven Ways to Grow Your Small Business

 Getting your business off the ground is challenging. Continuing to grow your business once it’s established is just as difficult.

And while generating new business and growing your customer base is necessary to succeed, it doesn’t happen overnight. It takes effective planning, strategy, and the willingness to get creative.

If your sales have recently hit a plateau, check out these 10 proven methods to continue growing your business.

1. Know your customers

Knowing who your customers are and what they need is vital. You went through the process of identifying a target market when developing your business plan. But now you have an active customer base that you need to engage with and in the process improve your business.

Whether it’s through a quarterly survey, user reviews, or direct customer service communications, you need to be asking for honest feedback. Take note of consistent grievances amongst your customer-base and use those to launch new features, make internal adjustments, or any number of fixes.

And while direct feedback from your customer base is invaluable, you need to also be paying attention to the market and your competitors. Conducting a market analysis on a regular basis ensures that you’re aware of any competitive moves and how different economic events may affect your customers. Combined with the insightful feedback from your customers, it provides a full picture of potential avenues for growth.

2. Focus on customer service

As you look to grow your business, quality customer service for your current customers can fall by the wayside. Sure customer churn is part of doing business, but you don’t want it to be a direct result of your attempts to grow. And you don’t want to compound people leaving by providing a poor experience.

At the same time, focusing on quality customer service can be a direct avenue for growth. If your current customers are treated exceptionally, they’ll be more likely to leave positive reviews, recommend you to their friends, and of course purchase from your business again.

3. Extend value from current customers

It’s common when looking for growth opportunities to immediately try and attract new customers, but what about your current ones? You’ve built credibility with them meaning they’re more likely to purchase from you again or even pay more for additional services and new products.

Explore opportunities to extend the value of your customers. Add a new product line that compliments previous purchases. Test increasing service prices in exchange for additional features, hands-on direction, or other additions that your customers find valuable.

Just because you’ve possibly hit the limit of growing your established target market, doesn’t mean that you can’t pull more value from it. And who knows, any changes you make to increase the value for current customers may be a springboard for bringing on new ones.

4. Leverage social media

Diving into social media can be daunting. But here’s the thing, you don’t have to have experience with it to leverage social platforms. It can be as simple as opening a business profile and beginning to grow a community of customers.

You don’t need to post every day or even create incredible looking images and videos, but do establish a consistent schedule your followers and customers can expect. From there it’s up to you to actively engage with your followers, read comments, answer messages, and generally build your social brand.

Overall it’s a great way to identify trends and insights about your customers. If you want, you can even use the insights you gain and try running social ads. It’s easier than you think and is an inexpensive way to test promotions, gauge the interest of a new customer base, or even run a full-fledged digital campaign.

5. Grow your team

Growing your customer base and growing your sales typically means growing your team. And just as you need to focus on providing exceptional customer service, you need to focus on the quality of the people that join your team.

Focus on finding diverse voices that can not only fulfill the duties of the role but that can provide unique perspectives that challenges your own. It’s harmful to have a staff full of “yes men” and can potentially lead to poor internal culture and self-serving decisions. Having a vast range of employees that differ in experience, background, beliefs, and specialties bring new perspectives to the table that would be nonexistent without them. Learn more about the meaning of siloed and follow the best tips in order to deal with it.

Additionally, as you look to bring on new employees, you’ll also want to focus on your current staff’s professional development. Show that you value them and their contribution to your business. Give them more opportunities to lead and collaborate, involve them in the goal-setting process, and even foot the bill for them to attend seminars and trainings.

The way you treat your employees will be reflected in the way you treat your customers. Start by optimizing internally and your business will grow from there.

6. Showcase your expertise

If you want to continue building clout amongst your customers and other businesses, you need to showcase your expertise. This means providing resources, hosting webinars, conducting research studies, and even running Q&A’s through your social channels. Find opportunities to share what you know, and present it as a free opportunity to learn and grow.

Just be sure to gather contact information or provide a link to a specific promotional page when you host an event or give access to a download. You’re not just showcasing expertise but using it to grow an audience that will hopefully one day turn into customers. Follow-up and keep providing valuable insight and you’ll be able to turn it into consistent growth.

Tags: bioinformatica, Database
17 settembre 2008 - 19:13

The Importance of a Friendly & Positive Environment in the Workplace

workplace

Cultivating positivity within the workplace pays huge intangible dividends that boost the company’s bottom line. Employees who love their jobs, enjoy their coworkers and appearance forward to the workday are more likely to try to do whatever they will to assist the corporate thrive. A positive workplace culture affirms the worth, dignity and pride of every employee, which benefits the individual.

Power of Positivity

Mutually shared core values include respect, kindness, patience and acceptance of 1 another. When positivity is the norm, employees offer to assist before being asked. They gather as a team to get ideas, set ambitious goals and strive for excellence. Change, innovation, inspiration and diverse angles are supported and embraced. Risk taking is inspired albeit the result falls in need of expectations. Equally, negative environments drain energy, maintain fear and spoil determination. Turnover is high and company constancy is low.

Positive Workplace Characteristics

A positive workplace goes beyond providing regular breaks, an opportunity room with vending machines, and an annual employee appreciation breakfast. news Daily suggests that employees are more likely to possess a positive attitude about work if the corporate culture is flexible and respects work-life balance. Employees also need suitable support, training, resources and space to execute their job. The mood is additionally influenced by overall workplace conditions like safety features, adequate lighting and cosy temperatures throughout the building.

Many of the factors that affect job performance are essential. After basic needs are met for a daily paycheck and a gentle job, employees want to feel that they’re doing meaningful work that matters to the corporate. Management style also affects how employees feel about coming to figure. Being micro-managed, scolded and belittled creates resistance, resentment and passive-aggressive behavior. against this, a supportive manager who invites employee input offers constructive feedback and consistently acknowledges employee contributions evokes trust and positivity. Learn more about transformational leadership theory defined.

Higher Productivity

According to Harvard Business Review, cutthroat, competitive corporate cultures stymie productivity, whereas, supportive work environments create conditions for business growth. Workers who pride themselves in what they are doing and where they work want to ascertain the corporate flourish. They ask what more they will do to assist the corporate move forward. Highly motivated employees are goal oriented and laser focused on measurable results. They welcome high standards and push themselves to succeed in key performance indicators on the schedule.

Tags: Bibliografia, bioinformatica