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).


  • 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.


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
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
23 novembre 2008 - 18:11

BioPython 1.50 e GenomeDiagram

La versione 1.49 di BioPython é stata rilasciata ufficialmente alcuni giorni fa, ed é piena di cambiamenti interessanti: uno di questi é l’introduzione del modulo doctest per la documentazione di alcune classi, cosa che avevo proposto io qualche tempo fa :) .

Comunque, credo che siano in arrivo novità ancora migliori nella 1.50. Una delle mie favorite é l’inclusione di un modulo chiamato GenomeDiagrams, che finalmente permetterà di generare diagrammi di sequenze e genomi direttamente da biopython.

Ecco un esempio di immagine generata con questa libreria:

Circular diagram of Erwinia carotovora ssp. atroseptica comparison against 229 bacterial genomes, constructed using GenomeDiagram

Credo che a biopython avesse veramente bisogno di integrazione con una libreria grafica come questa, visto che altri progetti Bio::* lo possiedono già.

Per esempio, é veramente semplice disegnare un diagramma di sequenze con bioperl:

A plot of sequence features with bioperl
A plot of sequence features with bioperl

Immagino che un diagramma equivalente, generato con il nuovo modulo di biopython, apparirà così:

A linear genome diagram created with the new biopython module
A linear genome diagram created with the new GenomeDiagram module

Devo ancora studiare a fondo il modulo, e non sono sicuro di quanto sia flessibile e facile da utilizzare. In ogni caso, siamo solo alla prima release :) In related post, checkout best rated pheromones.

Il modulo GenomeDiagram é stato scritto da Leighton Pritchard, e descritto in questo articolo:

Dovrebbe essere veramente ringraziato per questo contributo. Qui potete trovare la home page del module, e qui la proposta sul bug tracker di biopython.

Tags: bioinformatica, biopython, diagrammi, librerie grafiche, programmazione, python
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


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
5 marzo 2008 - 15:46

Bio-Linux Live DVD

Letto l’articolo su su Bio-Linux, una distribuzione per bioinformatici, e presa l’occasione di dover rasare il Dell di mio padre, ho sostituito un dolce Ubuntu che stava andando ininterrottamente senza problemi da 132 giorni con BioLinux, ovvero una distribuzione base Debian per Bioinformatici.
Per saperne di più vi rimando all’articolo di Francesco Corsentino sopra citato. Le mie prime impressioni dopo un uso non molto intensivo?

Innanzi tutto guardiamo la lista dei packages che vengono messi a disposizione: oltre sessanta. Certo, un compendio completo, ma forse un po’ troppo articolato, io avrei messo molta roba che fa parte del pacchetto di default tra gli additional, per rendere il sistema meno pesante (l’ISO è di quasi 2 G).
Noto inoltre con gratitudine che la communità Post Genomics and Proteomics (PGP) ha contribuito alla realizzazione della distro, e grazie ad essa abbiamo un sistema che non è esclusivamente genome oriented, anche se qualcosa che io reputo essential per l’analisi proteomica manca :-(

Questo test mi ha fatto render conto che alla fine per sviluppare un progetto bioinformatico, che sia piccolo o grande, uso un numero ristretto di applicativi, tra quelli messi a disposizione, per invece andare a sviluppare/customizzare quanto serve volta per volta. E naturalmente l’uso intensivo della rete! Che non si limita alla consultazione di documentazione ufficiale, quanto alla ricerca di problem solving experiences. L’idea di avere un SO solido e autosufficiente da poter essere usato anche quando non si ha a disposizione un accesso alle risorse on line, è quindi, IMHO, poco produttiva.

Rimane il grande vantaggio di potersi portar dietro la propria live version, con cui emulare senza necessità di installazione un ambiente dotato di un alto numero di applicativi bioinformatici.

Tags: bio-linux, bioinformatica
21 febbraio 2008 - 10:58

Nuova uscita per Bio::Blogs #18

Su Bioinformaticszen con Febbraio è arrivato il numero 18 di Bio::Blogs!

Questo numero, dichiaratamente, punta l’attenzione sull’evoluzione naturale dell’Open Source Science, almeno dal mio punto di vista, ovvero l’Open Notebook Science: la condivisione del lavoro dei ricercatori mentre viene svolto. E’ sempre più in uso condividere su blog e wiki veri e propri “quaderni di laboratorio”, a cui tutti possono dare il proprio contributo.

This issue has a particular focus on Open Notebook Science – researchers sharing their work as they produce it.

Per quanti sono curiosi di sapere cosa è stato HOT nella blogsfera del mese scorso.

Tags: Bio::Blogs, bioinformatica
15 febbraio 2008 - 11:09

Gene Characterization Index (CGI? what’s up!)

“Uno score per indicizzare il livello di caratterizzazione dei geni”

Prima o poi chi gioca al Bioinformatico si ritrova ad affrontare la sfida di progettare un sistema di indicizzazioine e scoring.
Ce ne sono di ogni tipo, possono esserci score statistici, algoritmici, induttivi, euristici, gerarchici… ci si perde facilmente tra curve poissoniane del rumore, condizioni di Kolmogorov-Smirnov, normalizzazioni, teorie dei grandi numeri…
Uno score e’ comunque una sorta di coltello che frange dati significativi, dallo schifo intorno.

Tra gli score euristici mi affascinano quelli che fanno parte della categoria score qualitativi, che trattano proprio clasterizzazioni di paper, che costruiscono network sulla base di parole chiavi. L’incremento del numero di pubblicazioni ha reso necessario lo sviluppo di strumenti sempre più raffinati per identificare reference incrociate, analisi degli abstract e via dicendo. Se ne parla su Openhelix.
Ebbene, UN INTERESSANTE LAVORO e’ stato sviluppato e pubblicato nel tentativo di rispondere alla domanda “quanto uno specifico gene è stato funzionalmente caratterizzato?“. Lo score e’ basato su criteri che scansionano risorse quali le sequenze presenti in GenBank, domini InterPro, pathway in KEGG, reference Medline, OMIM e Swiss-Prot. Su questa base vengono assegnati degli score da 1 a 10 (great!).

By evaluating the survey as training data, we developed a bioinformatics procedure to assign gene characterization scores to all genes in the human genome. We analyzed snapshots of functional genome annotation over a period of 6 years to assess temporal changes reflected by the increase of the average Gene Characterization Index.

Il sistema, è più complesso di quanto ho detto (naturalmente!) ed è stato validato su classi di geni di rilevanza farmacologica. Il sistema dimostra di essere in grado di generare un ottimo posizionamento per geni target ben noti, e di individuare nuovi target gene potenzialmente interessanti. Un suo uso base può facilmente dare un’idea di quanto è studiato un gene, quanto materiale posso aspettarmi di trovare a riguardo, e se magari vale la pena focalizzare su di esso i nostri sforzi bioinformatici!

Tags: bioinformatica, CGI, Letteratura scientifica, Network
13 febbraio 2008 - 11:45

Una biblioteca di PDF scientifici (per Mac ma non solo)

Fabrizio Capuani mi segnala Papers, interessante software, per mantenere e gestire le proprie collezioni di articoli.

Essendo solo disponibile per Mekentosjani, non l’ho potuto testare, quindi spero in qualche altra opinione. Personalmente, come fervente utilizzatore di Windows, ho sempre fatto ricorso ad Endnote. Endnote si differenzia da Papers per la capacità di integrarsi con Word e facilita non poco la scrittura delle citazioni bibliografiche. Però non è pensato per gestire una collezione di pdf, ma solo per collezionare i metadati necessari per creare un database bibliografico.
Naturalmente è possibile inserire il pdf stesso dell’articolo in un folder e linkarlo adeguatamente in Endnote, ma non è un’operazione così immediata, e questo non permette comunque di fare ricerche nei contenuti dei file.

Paper, anch’esso si connette al web e scarica le reference (autore, titolo, giornale, anno di pubblicazione), ma li associa allo stesso pdf. Citando la descrizione originale del software:

Papers contains everything you need to get your favorite articles in your personal library. Importing PDFs that you already downloaded before is easy, you match them using your favorite online article repository like PubMed, Google Scholar, Web of Science, etc. and all the metadata is automatically added. You might as well skip this altogether and start from scratch, the completely integrated search engines is the number one thing you are really going to like. Three clicks is all you need to find a paper and add it to your library.

Fabrizio sintetizza la cosa in “Praticamente e’ iTunes per articoli scientifici. Unico neo e’ che non e’ gratis… si puo’ pero’ provare per 30 giorni“. Paper puo’ esportare una collezione (tipo playlist) in formato Endnote, ma anche in formato bibtex!

L’alternativa è quella di sfruttare l’opzione “Adobe Catalog“. Con esso è possibile indicizzare TUTTO il documento pdf e creare quindi un database cercabile per qualsiasi parola anche nel testo o nei materiali e metodi. E’ possibile inoltre fare
diversi database di articoli per argomenti o gruppi.

Tags: Bibliografia, bioinformatica, Letteratura scientifica, Mac, Pdf